Starting phenix.real_space_refine on Wed Feb 12 01:16:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpo_32686/02_2025/7wpo_32686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpo_32686/02_2025/7wpo_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_32686/02_2025/7wpo_32686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpo_32686/02_2025/7wpo_32686.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpo_32686/02_2025/7wpo_32686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpo_32686/02_2025/7wpo_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-5592/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: 4.62, per 1000 atoms: 0.68 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: 2.21 Conformation dependent library (CDL) restraints added in 2.6 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: 0.70 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: 2.02 Time building geometry restraints manager: 2.65 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: 1.860 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- 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 : 0.806 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: 0.1989 time to fit residues: 50.8605 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 : 0.772 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119856 restraints weight = 11138.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123824 restraints weight = 5595.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126442 restraints weight = 3625.482| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.761 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8636 (t80) cc_final: 0.8258 (t80) REVERT: A 243 TYR cc_start: 0.8509 (t80) cc_final: 0.8206 (t80) REVERT: A 332 MET cc_start: 0.7562 (ttp) cc_final: 0.7297 (ttt) REVERT: A 568 TYR cc_start: 0.8874 (t80) cc_final: 0.8512 (t80) REVERT: A 640 TYR cc_start: 0.8268 (t80) cc_final: 0.7933 (t80) REVERT: A 651 ARG cc_start: 0.7211 (ttm-80) cc_final: 0.5184 (ttp-170) REVERT: B 532 ASN cc_start: 0.9134 (m-40) cc_final: 0.8788 (m-40) outliers start: 9 outliers final: 5 residues processed: 136 average time/residue: 0.1643 time to fit residues: 31.0646 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 : 0.801 ------------------------------------------------------------------------------- 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 82 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115852 restraints weight = 11613.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119643 restraints weight = 5908.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122046 restraints weight = 3854.287| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7007 Z= 0.212 Angle : 0.609 17.731 9543 Z= 0.312 Chirality : 0.042 0.227 1086 Planarity : 0.004 0.035 1197 Dihedral : 7.121 62.746 1286 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.77 % Allowed : 12.22 % Favored : 86.01 % 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: 1.64 (0.28), residues: 859 helix: 1.70 (0.24), residues: 446 sheet: -0.28 (0.51), residues: 93 loop : 0.85 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.013 0.001 PHE B 451 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG B 404 *********************** 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 125 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 201 ASP cc_start: 0.9239 (OUTLIER) cc_final: 0.8971 (t70) REVERT: A 243 TYR cc_start: 0.8607 (t80) cc_final: 0.8269 (t80) REVERT: A 281 LEU cc_start: 0.8738 (mt) cc_final: 0.8522 (mp) REVERT: A 332 MET cc_start: 0.7745 (ttp) cc_final: 0.7513 (ttt) REVERT: A 640 TYR cc_start: 0.8298 (t80) cc_final: 0.8092 (t80) REVERT: B 532 ASN cc_start: 0.9107 (m-40) cc_final: 0.8789 (m-40) outliers start: 11 outliers final: 7 residues processed: 117 average time/residue: 0.1407 time to fit residues: 24.1284 Evaluate side-chains 114 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 201 ASP 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 36 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114040 restraints weight = 11591.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117707 restraints weight = 5889.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120075 restraints weight = 3879.709| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7007 Z= 0.175 Angle : 0.561 14.051 9543 Z= 0.286 Chirality : 0.041 0.184 1086 Planarity : 0.004 0.038 1197 Dihedral : 6.121 49.982 1286 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.09 % Allowed : 12.70 % Favored : 85.21 % 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: 1.83 (0.29), residues: 859 helix: 1.92 (0.24), residues: 444 sheet: -0.25 (0.51), residues: 91 loop : 0.84 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.003 0.001 HIS A 159 PHE 0.013 0.001 PHE A 143 TYR 0.024 0.001 TYR A 568 ARG 0.005 0.000 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 129 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.8111 (m-30) cc_final: 0.7901 (m-30) REVERT: A 328 TRP cc_start: 0.8901 (m100) cc_final: 0.8694 (m100) REVERT: A 332 MET cc_start: 0.7775 (ttp) cc_final: 0.7531 (ttt) REVERT: A 455 MET cc_start: 0.8486 (tmm) cc_final: 0.7977 (tmm) REVERT: A 595 LEU cc_start: 0.8721 (mt) cc_final: 0.8515 (mp) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.1687 time to fit residues: 28.9779 Evaluate side-chains 110 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 36 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 417 HIS A 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102559 restraints weight = 11648.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105817 restraints weight = 6268.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107963 restraints weight = 4285.422| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 7007 Z= 0.408 Angle : 0.697 13.584 9543 Z= 0.356 Chirality : 0.047 0.196 1086 Planarity : 0.005 0.038 1197 Dihedral : 6.706 59.791 1286 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.57 % Allowed : 14.47 % Favored : 82.96 % 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: 1.36 (0.29), residues: 859 helix: 1.64 (0.24), residues: 444 sheet: -0.01 (0.53), residues: 82 loop : 0.27 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.013 0.002 PHE A 230 TYR 0.020 0.002 TYR A 237 ARG 0.009 0.001 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 119 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8747 (mt) REVERT: A 332 MET cc_start: 0.8109 (ttp) cc_final: 0.7857 (ttt) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.1821 time to fit residues: 27.9531 Evaluate side-chains 105 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 10 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.131845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106735 restraints weight = 11516.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110085 restraints weight = 5941.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112248 restraints weight = 3974.882| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4697 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= 0.187 Angle : 0.572 13.652 9543 Z= 0.291 Chirality : 0.041 0.181 1086 Planarity : 0.004 0.035 1197 Dihedral : 6.152 56.262 1286 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.57 % Allowed : 15.59 % Favored : 81.83 % 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: 1.65 (0.29), residues: 859 helix: 1.94 (0.24), residues: 446 sheet: -0.08 (0.54), residues: 81 loop : 0.36 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 163 HIS 0.003 0.001 HIS A 417 PHE 0.012 0.001 PHE A 516 TYR 0.025 0.001 TYR A 640 ARG 0.006 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: 16 poor density : 106 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8768 (mt) REVERT: A 332 MET cc_start: 0.7988 (ttp) cc_final: 0.7751 (ttt) REVERT: A 474 MET cc_start: 0.8734 (mmp) cc_final: 0.8488 (mmp) outliers start: 16 outliers final: 8 residues processed: 111 average time/residue: 0.1704 time to fit residues: 26.6020 Evaluate side-chains 116 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 457 SER 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 54 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.128420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104299 restraints weight = 11283.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107619 restraints weight = 5779.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109848 restraints weight = 3800.933| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7007 Z= 0.240 Angle : 0.586 13.264 9543 Z= 0.296 Chirality : 0.042 0.191 1086 Planarity : 0.004 0.033 1197 Dihedral : 6.003 58.283 1286 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.73 % Allowed : 16.08 % Favored : 81.19 % 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: 1.80 (0.29), residues: 859 helix: 2.06 (0.25), residues: 446 sheet: 0.20 (0.61), residues: 65 loop : 0.35 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 163 HIS 0.003 0.001 HIS A 417 PHE 0.018 0.002 PHE B 449 TYR 0.027 0.002 TYR A 640 ARG 0.005 0.001 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 120 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8787 (mt) REVERT: A 332 MET cc_start: 0.8027 (ttp) cc_final: 0.7772 (ttt) REVERT: A 474 MET cc_start: 0.8766 (mmp) cc_final: 0.8467 (mmp) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.1558 time to fit residues: 23.9135 Evaluate side-chains 113 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 0.0170 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.131014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107299 restraints weight = 11310.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110595 restraints weight = 5620.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112811 restraints weight = 3674.806| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7007 Z= 0.168 Angle : 0.559 12.689 9543 Z= 0.280 Chirality : 0.040 0.180 1086 Planarity : 0.003 0.032 1197 Dihedral : 5.682 56.412 1286 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.25 % Allowed : 16.56 % Favored : 81.19 % 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: 1.97 (0.30), residues: 859 helix: 2.21 (0.25), residues: 445 sheet: 0.15 (0.61), residues: 64 loop : 0.45 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 163 HIS 0.003 0.000 HIS A 417 PHE 0.014 0.001 PHE B 449 TYR 0.025 0.001 TYR A 640 ARG 0.005 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 123 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 332 MET cc_start: 0.7944 (ttp) cc_final: 0.7705 (ttt) REVERT: A 474 MET cc_start: 0.8731 (mmp) cc_final: 0.8489 (mmp) outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.1654 time to fit residues: 26.5658 Evaluate side-chains 113 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 22 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN B 471 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109394 restraints weight = 11314.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112858 restraints weight = 5712.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115115 restraints weight = 3700.813| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7007 Z= 0.155 Angle : 0.547 11.809 9543 Z= 0.272 Chirality : 0.039 0.173 1086 Planarity : 0.003 0.032 1197 Dihedral : 5.228 54.752 1286 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.77 % Allowed : 17.04 % Favored : 81.19 % 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: 2.08 (0.30), residues: 859 helix: 2.36 (0.25), residues: 445 sheet: -0.47 (0.59), residues: 72 loop : 0.60 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 163 HIS 0.001 0.000 HIS A 417 PHE 0.012 0.001 PHE B 392 TYR 0.027 0.001 TYR A 640 ARG 0.008 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 121 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 332 MET cc_start: 0.7940 (ttp) cc_final: 0.7692 (ttt) REVERT: A 474 MET cc_start: 0.8683 (mmp) cc_final: 0.8465 (mmp) REVERT: A 568 TYR cc_start: 0.8904 (t80) cc_final: 0.8336 (t80) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.1580 time to fit residues: 25.4863 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 : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 457 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.132942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108970 restraints weight = 11498.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112449 restraints weight = 5798.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114702 restraints weight = 3771.064| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7007 Z= 0.162 Angle : 0.553 12.519 9543 Z= 0.274 Chirality : 0.040 0.173 1086 Planarity : 0.003 0.032 1197 Dihedral : 5.078 54.851 1286 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.96 % Allowed : 17.68 % Favored : 81.35 % 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: 2.40 (0.25), residues: 445 sheet: -0.47 (0.59), residues: 72 loop : 0.63 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 163 HIS 0.002 0.000 HIS A 42 PHE 0.009 0.001 PHE A 523 TYR 0.023 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 110 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 332 MET cc_start: 0.7939 (ttp) cc_final: 0.7678 (ttt) REVERT: A 385 TYR cc_start: 0.8162 (p90) cc_final: 0.7957 (p90) REVERT: A 474 MET cc_start: 0.8679 (mmp) cc_final: 0.8442 (mmp) REVERT: A 568 TYR cc_start: 0.8929 (t80) cc_final: 0.8363 (t80) outliers start: 6 outliers final: 6 residues processed: 107 average time/residue: 0.1598 time to fit residues: 24.3264 Evaluate side-chains 109 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.131359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107495 restraints weight = 11384.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110928 restraints weight = 5751.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113181 restraints weight = 3740.786| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7007 Z= 0.176 Angle : 0.561 12.492 9543 Z= 0.277 Chirality : 0.040 0.192 1086 Planarity : 0.003 0.032 1197 Dihedral : 4.998 55.932 1286 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.64 % Allowed : 18.17 % Favored : 81.19 % 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: 2.37 (0.25), residues: 446 sheet: -0.46 (0.60), residues: 72 loop : 0.66 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.002 0.000 HIS A 374 PHE 0.012 0.001 PHE B 392 TYR 0.024 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: 2284.70 seconds wall clock time: 41 minutes 47.14 seconds (2507.14 seconds total)