Starting phenix.real_space_refine on Fri Jun 6 00:41:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpo_32686/06_2025/7wpo_32686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpo_32686/06_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_32686/06_2025/7wpo_32686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpo_32686/06_2025/7wpo_32686.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpo_32686/06_2025/7wpo_32686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpo_32686/06_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-5710/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: 4.42, per 1000 atoms: 0.65 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: 1.87 Conformation dependent library (CDL) restraints added in 888.1 milliseconds 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: 0.71 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: 1.84 Time building geometry restraints manager: 2.15 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: 1.830 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.020 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- 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 0.140 7030 Z= 0.792 Angle : 1.660 19.617 9606 Z= 1.120 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 Details of bonding type rmsd link_NAG-ASN : bond 0.07257 ( 9) link_NAG-ASN : angle 2.85549 ( 27) link_ALPHA1-6 : bond 0.08930 ( 1) link_ALPHA1-6 : angle 2.02385 ( 3) link_BETA1-4 : bond 0.06944 ( 5) link_BETA1-4 : angle 3.62684 ( 15) link_ALPHA1-3 : bond 0.07265 ( 1) link_ALPHA1-3 : angle 5.19512 ( 3) hydrogen bonds : bond 0.20719 ( 370) hydrogen bonds : angle 6.83225 ( 1023) link_BETA1-6 : bond 0.07465 ( 1) link_BETA1-6 : angle 2.53558 ( 3) SS BOND : bond 0.06069 ( 6) SS BOND : angle 2.98218 ( 12) covalent geometry : bond 0.01384 ( 7007) covalent geometry : angle 1.64492 ( 9543) *********************** 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 : 0.719 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: 0.1939 time to fit residues: 49.7507 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 : 0.763 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.9990 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: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.142553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118164 restraints weight = 10940.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122117 restraints weight = 5372.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124688 restraints weight = 3415.848| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7030 Z= 0.159 Angle : 0.663 8.109 9606 Z= 0.341 Chirality : 0.044 0.225 1086 Planarity : 0.004 0.032 1197 Dihedral : 7.826 70.782 1288 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 1.31 (0.28), residues: 859 helix: 1.30 (0.24), residues: 438 sheet: -0.20 (0.50), residues: 95 loop : 0.86 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 165 HIS 0.006 0.001 HIS A 42 PHE 0.017 0.002 PHE B 451 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 9) link_NAG-ASN : angle 3.36302 ( 27) link_ALPHA1-6 : bond 0.00326 ( 1) link_ALPHA1-6 : angle 1.99618 ( 3) link_BETA1-4 : bond 0.01013 ( 5) link_BETA1-4 : angle 2.20282 ( 15) link_ALPHA1-3 : bond 0.00857 ( 1) link_ALPHA1-3 : angle 2.72160 ( 3) hydrogen bonds : bond 0.06042 ( 370) hydrogen bonds : angle 4.61937 ( 1023) link_BETA1-6 : bond 0.00895 ( 1) link_BETA1-6 : angle 1.18279 ( 3) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.91247 ( 12) covalent geometry : bond 0.00339 ( 7007) covalent geometry : angle 0.62787 ( 9543) *********************** 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 : 0.769 Fit side-chains revert: symmetry clash REVERT: A 243 TYR cc_start: 0.8522 (t80) cc_final: 0.8218 (t80) REVERT: A 332 MET cc_start: 0.7570 (ttp) cc_final: 0.7304 (ttt) REVERT: A 568 TYR cc_start: 0.8883 (t80) cc_final: 0.8490 (t80) REVERT: A 640 TYR cc_start: 0.8256 (t80) cc_final: 0.7913 (t80) REVERT: A 651 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.5234 (ttp-170) REVERT: B 532 ASN cc_start: 0.9138 (m-40) cc_final: 0.8779 (m-40) outliers start: 9 outliers final: 5 residues processed: 134 average time/residue: 0.1613 time to fit residues: 30.1572 Evaluate side-chains 108 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 68 SER 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: 2.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 85 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.144323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119129 restraints weight = 11585.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122979 restraints weight = 5854.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125475 restraints weight = 3820.138| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7030 Z= 0.127 Angle : 0.628 16.548 9606 Z= 0.318 Chirality : 0.041 0.208 1086 Planarity : 0.004 0.036 1197 Dihedral : 7.063 61.637 1286 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.29 % Allowed : 11.41 % Favored : 87.30 % 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: 1.72 (0.24), residues: 447 sheet: -0.34 (0.50), residues: 95 loop : 0.86 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.002 0.001 HIS A 378 PHE 0.013 0.001 PHE B 451 TYR 0.017 0.001 TYR A 385 ARG 0.004 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 9) link_NAG-ASN : angle 2.30710 ( 27) link_ALPHA1-6 : bond 0.00231 ( 1) link_ALPHA1-6 : angle 1.81429 ( 3) link_BETA1-4 : bond 0.00659 ( 5) link_BETA1-4 : angle 1.48606 ( 15) link_ALPHA1-3 : bond 0.01195 ( 1) link_ALPHA1-3 : angle 1.93679 ( 3) hydrogen bonds : bond 0.04920 ( 370) hydrogen bonds : angle 4.21854 ( 1023) link_BETA1-6 : bond 0.00397 ( 1) link_BETA1-6 : angle 1.11445 ( 3) SS BOND : bond 0.00225 ( 6) SS BOND : angle 4.50582 ( 12) covalent geometry : bond 0.00262 ( 7007) covalent geometry : angle 0.59237 ( 9543) *********************** 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 127 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8700 (t70) REVERT: A 243 TYR cc_start: 0.8562 (t80) cc_final: 0.8227 (t80) REVERT: A 281 LEU cc_start: 0.8742 (mt) cc_final: 0.8519 (mp) REVERT: A 332 MET cc_start: 0.7608 (ttp) cc_final: 0.7381 (ttt) REVERT: A 640 TYR cc_start: 0.8211 (t80) cc_final: 0.8006 (t80) REVERT: B 532 ASN cc_start: 0.9100 (m-40) cc_final: 0.8803 (m-40) outliers start: 8 outliers final: 5 residues processed: 122 average time/residue: 0.1424 time to fit residues: 25.0878 Evaluate side-chains 112 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 201 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 399 ILE 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: 0.5980 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.140382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115074 restraints weight = 11631.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118757 restraints weight = 5956.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121240 restraints weight = 3899.757| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7030 Z= 0.124 Angle : 0.612 15.357 9606 Z= 0.304 Chirality : 0.041 0.180 1086 Planarity : 0.004 0.036 1197 Dihedral : 6.140 50.583 1286 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.57 % Allowed : 11.74 % Favored : 85.69 % 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: 1.79 (0.29), residues: 859 helix: 1.90 (0.24), residues: 447 sheet: -0.22 (0.52), residues: 91 loop : 0.78 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 PHE 0.014 0.001 PHE B 451 TYR 0.023 0.001 TYR A 568 ARG 0.004 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 9) link_NAG-ASN : angle 2.17304 ( 27) link_ALPHA1-6 : bond 0.00057 ( 1) link_ALPHA1-6 : angle 1.87007 ( 3) link_BETA1-4 : bond 0.00447 ( 5) link_BETA1-4 : angle 1.38233 ( 15) link_ALPHA1-3 : bond 0.01077 ( 1) link_ALPHA1-3 : angle 2.54775 ( 3) hydrogen bonds : bond 0.04349 ( 370) hydrogen bonds : angle 3.90808 ( 1023) link_BETA1-6 : bond 0.00144 ( 1) link_BETA1-6 : angle 1.31809 ( 3) SS BOND : bond 0.00319 ( 6) SS BOND : angle 4.94727 ( 12) covalent geometry : bond 0.00272 ( 7007) covalent geometry : angle 0.57072 ( 9543) *********************** 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 137 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 225 ASP cc_start: 0.8097 (m-30) cc_final: 0.7881 (m-30) REVERT: A 243 TYR cc_start: 0.8653 (t80) cc_final: 0.8341 (t80) REVERT: A 270 MET cc_start: 0.9236 (tpp) cc_final: 0.8953 (tpp) REVERT: A 328 TRP cc_start: 0.8882 (m100) cc_final: 0.8651 (m100) REVERT: A 332 MET cc_start: 0.7759 (ttp) cc_final: 0.7529 (ttt) REVERT: A 455 MET cc_start: 0.8461 (tmm) cc_final: 0.7942 (tmm) outliers start: 16 outliers final: 12 residues processed: 126 average time/residue: 0.1631 time to fit residues: 28.7978 Evaluate side-chains 118 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 134 CYS 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 A residue 539 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 468 VAL 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: 1.9990 chunk 71 optimal weight: 9.9990 chunk 26 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106311 restraints weight = 11537.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109714 restraints weight = 6095.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111936 restraints weight = 4107.732| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7030 Z= 0.199 Angle : 0.665 13.862 9606 Z= 0.333 Chirality : 0.044 0.185 1086 Planarity : 0.004 0.036 1197 Dihedral : 6.253 54.430 1286 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.73 % Allowed : 13.02 % 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: 1.59 (0.28), residues: 859 helix: 1.75 (0.24), residues: 444 sheet: 0.18 (0.53), residues: 81 loop : 0.48 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 163 HIS 0.007 0.001 HIS A 42 PHE 0.014 0.002 PHE B 451 TYR 0.020 0.002 TYR A 640 ARG 0.007 0.001 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 9) link_NAG-ASN : angle 2.37123 ( 27) link_ALPHA1-6 : bond 0.00197 ( 1) link_ALPHA1-6 : angle 1.99468 ( 3) link_BETA1-4 : bond 0.00442 ( 5) link_BETA1-4 : angle 1.54132 ( 15) link_ALPHA1-3 : bond 0.01140 ( 1) link_ALPHA1-3 : angle 3.02587 ( 3) hydrogen bonds : bond 0.05307 ( 370) hydrogen bonds : angle 4.13919 ( 1023) link_BETA1-6 : bond 0.00233 ( 1) link_BETA1-6 : angle 1.41954 ( 3) SS BOND : bond 0.00355 ( 6) SS BOND : angle 4.55272 ( 12) covalent geometry : bond 0.00459 ( 7007) covalent geometry : angle 0.62816 ( 9543) *********************** 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 123 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8636 (mt) REVERT: A 332 MET cc_start: 0.8055 (ttp) cc_final: 0.7772 (ttt) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 0.1739 time to fit residues: 28.0469 Evaluate side-chains 113 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 398 THR 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 10 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS B 471 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108413 restraints weight = 11509.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111900 restraints weight = 6002.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114161 restraints weight = 3987.886| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7030 Z= 0.128 Angle : 0.604 13.144 9606 Z= 0.300 Chirality : 0.041 0.181 1086 Planarity : 0.004 0.033 1197 Dihedral : 5.905 52.344 1286 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.77 % Allowed : 15.11 % Favored : 83.12 % 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: 1.79 (0.29), residues: 859 helix: 2.01 (0.24), residues: 443 sheet: 0.05 (0.53), residues: 81 loop : 0.48 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 163 HIS 0.002 0.001 HIS A 378 PHE 0.020 0.001 PHE B 449 TYR 0.015 0.001 TYR A 385 ARG 0.005 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 9) link_NAG-ASN : angle 2.20794 ( 27) link_ALPHA1-6 : bond 0.00066 ( 1) link_ALPHA1-6 : angle 1.83848 ( 3) link_BETA1-4 : bond 0.00381 ( 5) link_BETA1-4 : angle 1.32679 ( 15) link_ALPHA1-3 : bond 0.01248 ( 1) link_ALPHA1-3 : angle 2.57343 ( 3) hydrogen bonds : bond 0.04528 ( 370) hydrogen bonds : angle 3.95562 ( 1023) link_BETA1-6 : bond 0.00009 ( 1) link_BETA1-6 : angle 1.35159 ( 3) SS BOND : bond 0.00395 ( 6) SS BOND : angle 4.48027 ( 12) covalent geometry : bond 0.00291 ( 7007) covalent geometry : angle 0.56738 ( 9543) *********************** 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 118 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8952 (mm) cc_final: 0.8692 (mt) REVERT: A 332 MET cc_start: 0.8009 (ttp) cc_final: 0.7776 (ttt) outliers start: 11 outliers final: 8 residues processed: 111 average time/residue: 0.2330 time to fit residues: 37.3063 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 : 1.382 ------------------------------------------------------------------------------- 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 398 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 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS B 471 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109733 restraints weight = 11441.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113262 restraints weight = 5974.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115358 restraints weight = 3961.382| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7030 Z= 0.117 Angle : 0.581 12.293 9606 Z= 0.287 Chirality : 0.040 0.180 1086 Planarity : 0.004 0.033 1197 Dihedral : 5.571 51.709 1286 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.09 % Allowed : 15.11 % 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: 2.05 (0.29), residues: 859 helix: 2.24 (0.25), residues: 443 sheet: 0.31 (0.61), residues: 64 loop : 0.54 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 163 HIS 0.002 0.000 HIS A 241 PHE 0.013 0.001 PHE B 426 TYR 0.015 0.001 TYR A 385 ARG 0.008 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 9) link_NAG-ASN : angle 2.02623 ( 27) link_ALPHA1-6 : bond 0.00219 ( 1) link_ALPHA1-6 : angle 1.71713 ( 3) link_BETA1-4 : bond 0.00429 ( 5) link_BETA1-4 : angle 1.24534 ( 15) link_ALPHA1-3 : bond 0.01300 ( 1) link_ALPHA1-3 : angle 2.50989 ( 3) hydrogen bonds : bond 0.04152 ( 370) hydrogen bonds : angle 3.89862 ( 1023) link_BETA1-6 : bond 0.00077 ( 1) link_BETA1-6 : angle 1.31192 ( 3) SS BOND : bond 0.00494 ( 6) SS BOND : angle 4.31515 ( 12) covalent geometry : bond 0.00261 ( 7007) covalent geometry : angle 0.54697 ( 9543) *********************** 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 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9046 (ttp) cc_final: 0.8833 (ttm) REVERT: A 188 ASN cc_start: 0.8942 (t0) cc_final: 0.8561 (t0) REVERT: A 267 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8699 (mt) REVERT: A 332 MET cc_start: 0.7950 (ttp) cc_final: 0.7716 (ttt) outliers start: 13 outliers final: 11 residues processed: 113 average time/residue: 0.1755 time to fit residues: 28.7963 Evaluate side-chains 114 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 471 ASN 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 68 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 23 optimal weight: 0.0870 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS B 471 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109735 restraints weight = 11581.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113238 restraints weight = 5989.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115606 restraints weight = 3960.594| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7030 Z= 0.118 Angle : 0.590 12.192 9606 Z= 0.291 Chirality : 0.040 0.181 1086 Planarity : 0.004 0.032 1197 Dihedral : 5.454 51.680 1286 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.09 % Allowed : 15.59 % 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: 2.08 (0.29), residues: 859 helix: 2.30 (0.25), residues: 443 sheet: 0.26 (0.62), residues: 64 loop : 0.51 (0.35), residues: 352 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 0.010 0.001 PHE B 449 TYR 0.015 0.001 TYR A 385 ARG 0.006 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 9) link_NAG-ASN : angle 2.00075 ( 27) link_ALPHA1-6 : bond 0.00212 ( 1) link_ALPHA1-6 : angle 1.70809 ( 3) link_BETA1-4 : bond 0.00454 ( 5) link_BETA1-4 : angle 1.26095 ( 15) link_ALPHA1-3 : bond 0.01199 ( 1) link_ALPHA1-3 : angle 2.44642 ( 3) hydrogen bonds : bond 0.04085 ( 370) hydrogen bonds : angle 3.86850 ( 1023) link_BETA1-6 : bond 0.00074 ( 1) link_BETA1-6 : angle 1.31828 ( 3) SS BOND : bond 0.00409 ( 6) SS BOND : angle 4.49121 ( 12) covalent geometry : bond 0.00269 ( 7007) covalent geometry : angle 0.55537 ( 9543) *********************** 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: 13 poor density : 110 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8907 (t0) cc_final: 0.8546 (t0) REVERT: A 267 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 332 MET cc_start: 0.7947 (ttp) cc_final: 0.7712 (ttt) REVERT: A 385 TYR cc_start: 0.8447 (p90) cc_final: 0.8180 (p90) outliers start: 13 outliers final: 9 residues processed: 116 average time/residue: 0.3023 time to fit residues: 50.6722 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 : 0.842 ------------------------------------------------------------------------------- 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 134 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 471 ASN Chi-restraints excluded: chain B residue 510 THR 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: 4.9990 chunk 85 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS B 471 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108431 restraints weight = 11449.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111869 restraints weight = 5961.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114281 restraints weight = 3962.885| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7030 Z= 0.116 Angle : 0.598 12.300 9606 Z= 0.291 Chirality : 0.040 0.179 1086 Planarity : 0.003 0.032 1197 Dihedral : 5.325 51.490 1286 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.93 % Allowed : 16.24 % Favored : 81.83 % 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: 2.07 (0.30), residues: 859 helix: 2.32 (0.25), residues: 445 sheet: 0.22 (0.62), residues: 64 loop : 0.45 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 163 HIS 0.002 0.000 HIS A 417 PHE 0.010 0.001 PHE B 449 TYR 0.015 0.001 TYR A 385 ARG 0.006 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 9) link_NAG-ASN : angle 1.95359 ( 27) link_ALPHA1-6 : bond 0.00139 ( 1) link_ALPHA1-6 : angle 1.64093 ( 3) link_BETA1-4 : bond 0.00405 ( 5) link_BETA1-4 : angle 1.21389 ( 15) link_ALPHA1-3 : bond 0.01228 ( 1) link_ALPHA1-3 : angle 2.38995 ( 3) hydrogen bonds : bond 0.04010 ( 370) hydrogen bonds : angle 3.85605 ( 1023) link_BETA1-6 : bond 0.00127 ( 1) link_BETA1-6 : angle 1.32678 ( 3) SS BOND : bond 0.00441 ( 6) SS BOND : angle 4.42553 ( 12) covalent geometry : bond 0.00262 ( 7007) covalent geometry : angle 0.56491 ( 9543) *********************** 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 120 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8929 (t0) cc_final: 0.8543 (t0) REVERT: A 267 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8718 (mt) REVERT: A 332 MET cc_start: 0.7939 (ttp) cc_final: 0.7695 (ttt) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.1930 time to fit residues: 31.0340 Evaluate side-chains 117 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 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 59 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 11 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 0.0000 chunk 62 optimal weight: 8.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109852 restraints weight = 11453.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113269 restraints weight = 5808.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115636 restraints weight = 3792.435| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7030 Z= 0.112 Angle : 0.593 12.430 9606 Z= 0.290 Chirality : 0.040 0.176 1086 Planarity : 0.003 0.032 1197 Dihedral : 5.198 51.169 1286 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.61 % Allowed : 16.56 % Favored : 81.83 % 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: 2.36 (0.25), residues: 445 sheet: 0.17 (0.62), residues: 64 loop : 0.50 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 163 HIS 0.001 0.000 HIS A 417 PHE 0.009 0.001 PHE A 516 TYR 0.017 0.001 TYR A 51 ARG 0.006 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 9) link_NAG-ASN : angle 1.91882 ( 27) link_ALPHA1-6 : bond 0.00349 ( 1) link_ALPHA1-6 : angle 1.64657 ( 3) link_BETA1-4 : bond 0.00428 ( 5) link_BETA1-4 : angle 1.20325 ( 15) link_ALPHA1-3 : bond 0.01257 ( 1) link_ALPHA1-3 : angle 2.33889 ( 3) hydrogen bonds : bond 0.03903 ( 370) hydrogen bonds : angle 3.84247 ( 1023) link_BETA1-6 : bond 0.00129 ( 1) link_BETA1-6 : angle 1.28867 ( 3) SS BOND : bond 0.00366 ( 6) SS BOND : angle 4.33014 ( 12) covalent geometry : bond 0.00250 ( 7007) covalent geometry : angle 0.56108 ( 9543) ********************** 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 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: A 188 ASN cc_start: 0.8839 (t0) cc_final: 0.8469 (t0) REVERT: A 267 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8722 (mt) REVERT: A 332 MET cc_start: 0.7907 (ttp) cc_final: 0.7667 (ttt) REVERT: A 385 TYR cc_start: 0.8196 (p90) cc_final: 0.7770 (p90) outliers start: 10 outliers final: 9 residues processed: 110 average time/residue: 0.1624 time to fit residues: 25.3613 Evaluate side-chains 113 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 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 10 optimal weight: 0.1980 chunk 78 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109466 restraints weight = 11485.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113074 restraints weight = 5933.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115436 restraints weight = 3918.114| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7030 Z= 0.109 Angle : 0.592 12.463 9606 Z= 0.288 Chirality : 0.040 0.171 1086 Planarity : 0.003 0.031 1197 Dihedral : 5.073 50.726 1286 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.77 % Allowed : 16.24 % Favored : 81.99 % 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: 2.17 (0.30), residues: 859 helix: 2.41 (0.25), residues: 444 sheet: 0.03 (0.62), residues: 66 loop : 0.55 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 163 HIS 0.001 0.000 HIS A 374 PHE 0.009 0.001 PHE A 516 TYR 0.019 0.001 TYR A 51 ARG 0.006 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 9) link_NAG-ASN : angle 1.88131 ( 27) link_ALPHA1-6 : bond 0.00371 ( 1) link_ALPHA1-6 : angle 1.61158 ( 3) link_BETA1-4 : bond 0.00425 ( 5) link_BETA1-4 : angle 1.18620 ( 15) link_ALPHA1-3 : bond 0.01281 ( 1) link_ALPHA1-3 : angle 2.29280 ( 3) hydrogen bonds : bond 0.03807 ( 370) hydrogen bonds : angle 3.84673 ( 1023) link_BETA1-6 : bond 0.00132 ( 1) link_BETA1-6 : angle 1.29295 ( 3) SS BOND : bond 0.00299 ( 6) SS BOND : angle 4.26255 ( 12) covalent geometry : bond 0.00240 ( 7007) covalent geometry : angle 0.56075 ( 9543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.59 seconds wall clock time: 51 minutes 13.92 seconds (3073.92 seconds total)