Starting phenix.real_space_refine on Fri Dec 27 23:10:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpo_32686/12_2024/7wpo_32686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpo_32686/12_2024/7wpo_32686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpo_32686/12_2024/7wpo_32686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpo_32686/12_2024/7wpo_32686.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpo_32686/12_2024/7wpo_32686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpo_32686/12_2024/7wpo_32686.cif" } resolution = 3.5 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= 0.005 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4371 2.51 5 N 1155 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6829 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5279 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 27, 'TRANS': 652} Chain breaks: 1 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 34, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1325 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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 Time building chain proxies: 4.98, per 1000 atoms: 0.73 Number of scatterers: 6829 At special positions: 0 Unit cell: (95.94, 87.74, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1263 8.00 N 1155 7.00 C 4371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 142 " distance=2.17 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.07 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 410 " distance=2.02 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 526 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 432 " " NAG A 802 " - " ASN A 91 " " NAG A 803 " - " ASN A 688 " " NAG A 804 " - " ASN A 546 " " NAG B 601 " - " ASN B 488 " " NAG C 1 " - " ASN A 54 " " NAG E 1 " - " ASN A 104 " " NAG G 1 " - " ASN A 280 " " NAG P 1 " - " ASN A 329 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 58.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.792A pdb=" N GLU A 88 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.763A pdb=" N GLN A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.757A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 4.100A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.944A 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 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 233 through 249 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: 4.431A pdb=" N ASN A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.619A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.753A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.847A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 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 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.950A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.618A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 635 through 656 Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.813A pdb=" N SER B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 452 through 460 removed outlier: 4.944A pdb=" N SER B 457 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 523 through 531 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.203A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 620 Processing sheet with id=AA6, first strand: chain 'B' and resid 403 through 407 removed outlier: 3.536A pdb=" N LEU B 564 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.451A pdb=" N SER B 552 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS B 505 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG B 550 " --> pdb=" O CYS B 505 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR B 507 " --> pdb=" O PRO B 548 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1109 1.31 - 1.45: 2091 1.45 - 1.59: 3733 1.59 - 1.72: 8 1.72 - 1.86: 66 Bond restraints: 7007 Sorted by residual: bond pdb=" N PRO A 583 " pdb=" CD PRO A 583 " ideal model delta sigma weight residual 1.473 1.349 0.124 1.40e-02 5.10e+03 7.88e+01 bond pdb=" CA ASN A 658 " pdb=" C ASN A 658 " ideal model delta sigma weight residual 1.524 1.614 -0.090 1.40e-02 5.10e+03 4.16e+01 bond pdb=" CA ASN A 330 " pdb=" C ASN A 330 " ideal model delta sigma weight residual 1.523 1.604 -0.081 1.37e-02 5.33e+03 3.51e+01 bond pdb=" C ASN A 329 " pdb=" O ASN A 329 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.23e-02 6.61e+03 2.15e+01 bond pdb=" CB LEU A 456 " pdb=" CG LEU A 456 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 7002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 9231 3.92 - 7.85: 271 7.85 - 11.77: 33 11.77 - 15.69: 5 15.69 - 19.62: 3 Bond angle restraints: 9543 Sorted by residual: angle pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" C LEU A 222 " ideal model delta sigma weight residual 111.36 97.31 14.05 1.09e+00 8.42e-01 1.66e+02 angle pdb=" N ASN A 330 " pdb=" CA ASN A 330 " pdb=" C ASN A 330 " ideal model delta sigma weight residual 112.23 126.64 -14.41 1.26e+00 6.30e-01 1.31e+02 angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 110.41 122.93 -12.52 1.23e+00 6.61e-01 1.04e+02 angle pdb=" N ALA A 701 " pdb=" CA ALA A 701 " pdb=" C ALA A 701 " ideal model delta sigma weight residual 111.07 100.55 10.52 1.07e+00 8.73e-01 9.67e+01 angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 113.88 102.89 10.99 1.23e+00 6.61e-01 7.98e+01 ... (remaining 9538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 4199 21.33 - 42.65: 107 42.65 - 63.98: 14 63.98 - 85.31: 13 85.31 - 106.63: 4 Dihedral angle restraints: 4337 sinusoidal: 1780 harmonic: 2557 Sorted by residual: dihedral pdb=" CB CYS B 386 " pdb=" SG CYS B 386 " pdb=" SG CYS B 410 " pdb=" CB CYS B 410 " ideal model delta sinusoidal sigma weight residual 93.00 39.32 53.68 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" N VAL A 293 " pdb=" C VAL A 293 " pdb=" CA VAL A 293 " pdb=" CB VAL A 293 " ideal model delta harmonic sigma weight residual 123.40 108.02 15.38 0 2.50e+00 1.60e-01 3.78e+01 dihedral pdb=" C ILE A 291 " pdb=" N ILE A 291 " pdb=" CA ILE A 291 " pdb=" CB ILE A 291 " ideal model delta harmonic sigma weight residual -122.00 -109.69 -12.31 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 4334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 807 0.106 - 0.212: 208 0.212 - 0.319: 45 0.319 - 0.425: 22 0.425 - 0.531: 4 Chirality restraints: 1086 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 MAN C 5 " pdb=" O6 BMA C 3 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.52e+01 chirality pdb=" C1 FUC P 3 " pdb=" O6 NAG P 1 " pdb=" C2 FUC P 3 " pdb=" O5 FUC P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.07e+01 ... (remaining 1083 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.046 2.00e-02 2.50e+03 4.91e-02 3.01e+01 pdb=" CG ASN A 329 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 315 " -0.054 2.00e-02 2.50e+03 2.99e-02 1.79e+01 pdb=" CG TYR A 315 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 315 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 315 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 315 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 315 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 315 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 315 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 432 " 0.032 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" CG ASN A 432 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 432 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 432 " -0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A 801 " 0.042 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2404 2.87 - 3.38: 6468 3.38 - 3.88: 11286 3.88 - 4.39: 13258 4.39 - 4.90: 21324 Nonbonded interactions: 54740 Sorted by model distance: nonbonded pdb=" OD1 ASP A 700 " pdb=" N ALA A 701 " model vdw 2.359 3.120 nonbonded pdb=" NZ LYS A 187 " pdb=" OD2 ASP A 509 " model vdw 2.441 3.120 nonbonded pdb=" O ILE B 491 " pdb=" N ILE B 493 " model vdw 2.442 3.120 nonbonded pdb=" O ARG A 575 " pdb=" CG2 THR A 576 " model vdw 2.445 3.460 nonbonded pdb=" N ASP A 292 " pdb=" O ASP A 292 " model vdw 2.446 2.496 ... (remaining 54735 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 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.060 Set scattering table: 0.070 Process input model: 23.000 Find NCS groups from input model: 0.070 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.014 0.124 7007 Z= 0.902 Angle : 1.645 19.617 9543 Z= 1.119 Chirality : 0.112 0.531 1086 Planarity : 0.006 0.049 1197 Dihedral : 11.403 106.634 2669 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.56 % Favored : 97.32 % Rotamer: Outliers : 0.48 % Allowed : 1.77 % Favored : 97.75 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 859 helix: -0.21 (0.22), residues: 431 sheet: 0.95 (0.53), residues: 77 loop : 0.07 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP A 203 HIS 0.004 0.001 HIS A 401 PHE 0.033 0.004 PHE B 451 TYR 0.054 0.005 TYR A 315 ARG 0.005 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8102 (t80) cc_final: 0.7811 (t80) REVERT: A 506 VAL cc_start: 0.8447 (t) cc_final: 0.8245 (t) REVERT: A 651 ARG cc_start: 0.6204 (ttm-80) cc_final: 0.4840 (ttt180) outliers start: 3 outliers final: 1 residues processed: 196 average time/residue: 0.2047 time to fit residues: 52.3015 Evaluate side-chains 111 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 103 GLN A 141 GLN A 159 HIS A 221 GLN A 635 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7007 Z= 0.201 Angle : 0.628 8.294 9543 Z= 0.330 Chirality : 0.044 0.206 1086 Planarity : 0.004 0.034 1197 Dihedral : 7.692 68.415 1288 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.45 % Allowed : 9.97 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 859 helix: 1.29 (0.24), residues: 438 sheet: -0.21 (0.50), residues: 95 loop : 0.85 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 165 HIS 0.005 0.001 HIS A 42 PHE 0.016 0.002 PHE B 451 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8208 (t80) cc_final: 0.7826 (t80) REVERT: A 243 TYR cc_start: 0.8530 (t80) cc_final: 0.8161 (t80) REVERT: A 568 TYR cc_start: 0.8499 (t80) cc_final: 0.8233 (t80) REVERT: A 640 TYR cc_start: 0.7415 (t80) cc_final: 0.7194 (t80) REVERT: A 651 ARG cc_start: 0.6435 (ttm-80) cc_final: 0.4837 (ttp-170) REVERT: B 532 ASN cc_start: 0.8956 (m-40) cc_final: 0.8743 (m-40) outliers start: 9 outliers final: 5 residues processed: 136 average time/residue: 0.1776 time to fit residues: 34.0970 Evaluate side-chains 106 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 7007 Z= 0.236 Angle : 0.611 15.508 9543 Z= 0.314 Chirality : 0.043 0.257 1086 Planarity : 0.004 0.035 1197 Dihedral : 7.091 62.328 1286 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.77 % Allowed : 12.38 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.68 (0.28), residues: 859 helix: 1.69 (0.24), residues: 446 sheet: 0.33 (0.54), residues: 81 loop : 0.71 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.004 0.001 HIS A 378 PHE 0.013 0.001 PHE B 451 TYR 0.015 0.002 TYR A 385 ARG 0.005 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 243 TYR cc_start: 0.8635 (t80) cc_final: 0.8303 (t80) REVERT: A 328 TRP cc_start: 0.8955 (m100) cc_final: 0.8649 (m100) REVERT: A 455 MET cc_start: 0.8355 (tmm) cc_final: 0.7862 (tmm) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 0.1559 time to fit residues: 26.5564 Evaluate side-chains 111 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 539 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 241 HIS A 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7007 Z= 0.240 Angle : 0.608 14.423 9543 Z= 0.308 Chirality : 0.043 0.178 1086 Planarity : 0.004 0.038 1197 Dihedral : 6.432 53.682 1286 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.57 % Allowed : 13.18 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.71 (0.29), residues: 859 helix: 1.80 (0.24), residues: 445 sheet: 0.31 (0.54), residues: 79 loop : 0.59 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 PHE 0.019 0.002 PHE A 84 TYR 0.022 0.002 TYR A 568 ARG 0.005 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8709 (mt) outliers start: 16 outliers final: 12 residues processed: 110 average time/residue: 0.1984 time to fit residues: 31.2469 Evaluate side-chains 108 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7007 Z= 0.175 Angle : 0.561 13.647 9543 Z= 0.283 Chirality : 0.040 0.182 1086 Planarity : 0.004 0.034 1197 Dihedral : 6.021 49.855 1286 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 13.50 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.29), residues: 859 helix: 2.10 (0.24), residues: 441 sheet: 0.46 (0.59), residues: 64 loop : 0.60 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.002 0.000 HIS A 42 PHE 0.012 0.001 PHE A 84 TYR 0.023 0.001 TYR A 640 ARG 0.006 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 105 average time/residue: 0.1661 time to fit residues: 24.6498 Evaluate side-chains 110 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7007 Z= 0.165 Angle : 0.540 12.327 9543 Z= 0.270 Chirality : 0.040 0.182 1086 Planarity : 0.004 0.033 1197 Dihedral : 5.506 49.145 1286 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.25 % Allowed : 14.31 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.29), residues: 859 helix: 2.16 (0.25), residues: 447 sheet: 0.43 (0.60), residues: 64 loop : 0.56 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.002 0.000 HIS A 374 PHE 0.017 0.001 PHE A 84 TYR 0.016 0.001 TYR A 640 ARG 0.009 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 112 average time/residue: 0.1503 time to fit residues: 24.6584 Evaluate side-chains 113 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.0670 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7007 Z= 0.154 Angle : 0.540 12.429 9543 Z= 0.267 Chirality : 0.039 0.176 1086 Planarity : 0.003 0.032 1197 Dihedral : 5.248 47.943 1286 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.29 % Allowed : 15.92 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.30), residues: 859 helix: 2.33 (0.25), residues: 445 sheet: 0.35 (0.62), residues: 64 loop : 0.53 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.002 0.000 HIS A 378 PHE 0.018 0.001 PHE B 449 TYR 0.026 0.001 TYR A 640 ARG 0.006 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 TYR cc_start: 0.8099 (p90) cc_final: 0.7822 (p90) outliers start: 8 outliers final: 7 residues processed: 109 average time/residue: 0.1470 time to fit residues: 23.2693 Evaluate side-chains 111 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.0670 chunk 16 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7007 Z= 0.156 Angle : 0.541 12.581 9543 Z= 0.266 Chirality : 0.039 0.176 1086 Planarity : 0.003 0.032 1197 Dihedral : 5.059 47.831 1286 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.61 % Allowed : 15.59 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.30), residues: 859 helix: 2.38 (0.25), residues: 445 sheet: 0.39 (0.63), residues: 64 loop : 0.57 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.002 0.000 HIS A 417 PHE 0.013 0.001 PHE B 449 TYR 0.026 0.001 TYR A 640 ARG 0.008 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7184 (m) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.1642 time to fit residues: 26.8894 Evaluate side-chains 111 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain B residue 510 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.0060 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7007 Z= 0.159 Angle : 0.547 12.165 9543 Z= 0.268 Chirality : 0.039 0.173 1086 Planarity : 0.003 0.031 1197 Dihedral : 4.902 48.005 1286 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.77 % Allowed : 15.92 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.30), residues: 859 helix: 2.36 (0.25), residues: 446 sheet: 0.16 (0.61), residues: 66 loop : 0.66 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.002 0.000 HIS A 378 PHE 0.010 0.001 PHE B 449 TYR 0.027 0.001 TYR A 640 ARG 0.007 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 MET cc_start: 0.7622 (mmm) cc_final: 0.7094 (mmm) REVERT: A 385 TYR cc_start: 0.7931 (p90) cc_final: 0.7701 (p90) outliers start: 11 outliers final: 8 residues processed: 110 average time/residue: 0.1523 time to fit residues: 24.3856 Evaluate side-chains 111 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.0050 chunk 20 optimal weight: 3.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7007 Z= 0.179 Angle : 0.564 11.738 9543 Z= 0.276 Chirality : 0.040 0.171 1086 Planarity : 0.003 0.032 1197 Dihedral : 4.854 48.715 1286 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.29 % Allowed : 16.08 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.30), residues: 859 helix: 2.40 (0.25), residues: 446 sheet: 0.11 (0.61), residues: 66 loop : 0.68 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.002 0.000 HIS A 374 PHE 0.011 0.001 PHE A 84 TYR 0.025 0.001 TYR A 640 ARG 0.007 0.000 ARG B 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 366 MET cc_start: 0.7662 (mmm) cc_final: 0.7204 (mmm) outliers start: 8 outliers final: 8 residues processed: 108 average time/residue: 0.1620 time to fit residues: 25.3459 Evaluate side-chains 108 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110458 restraints weight = 11185.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113908 restraints weight = 5634.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116190 restraints weight = 3656.312| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7007 Z= 0.174 Angle : 0.552 11.611 9543 Z= 0.274 Chirality : 0.040 0.168 1086 Planarity : 0.003 0.031 1197 Dihedral : 4.820 49.111 1286 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.13 % Allowed : 16.40 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.30), residues: 859 helix: 2.40 (0.25), residues: 446 sheet: 0.12 (0.61), residues: 66 loop : 0.68 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.002 0.000 HIS A 374 PHE 0.012 0.001 PHE A 84 TYR 0.025 0.001 TYR A 640 ARG 0.007 0.000 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.78 seconds wall clock time: 31 minutes 24.19 seconds (1884.19 seconds total)