Starting phenix.real_space_refine on Tue Mar 3 14:53:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ddp_30653/03_2026/7ddp_30653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ddp_30653/03_2026/7ddp_30653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ddp_30653/03_2026/7ddp_30653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ddp_30653/03_2026/7ddp_30653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ddp_30653/03_2026/7ddp_30653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ddp_30653/03_2026/7ddp_30653.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4143 2.51 5 N 1065 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6477 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "C" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1529 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.29, per 1000 atoms: 0.35 Number of scatterers: 6477 At special positions: 0 Unit cell: (102.356, 97.3875, 105.338, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1231 8.00 N 1065 7.00 C 4143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 53 " " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 408.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 56.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.030A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.596A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.529A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.806A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.205A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 219 through 252 removed outlier: 4.122A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.775A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.623A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.708A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (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 400 through 414 removed outlier: 3.557A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 532 removed outlier: 4.283A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.098A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.726A pdb=" N VAL 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 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.335A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.680A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.784A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.523A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.328A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.540A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 310 hydrogen bonds defined for protein. 881 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: 1.05 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2071 1.35 - 1.46: 1708 1.46 - 1.58: 2820 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6657 Sorted by residual: bond pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.21e-02 6.83e+03 9.23e+00 bond pdb=" N PHE C 456 " pdb=" CA PHE C 456 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.41e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 ... (remaining 6652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 8793 1.42 - 2.83: 209 2.83 - 4.25: 32 4.25 - 5.67: 14 5.67 - 7.09: 2 Bond angle restraints: 9050 Sorted by residual: angle pdb=" N VAL A 318 " pdb=" CA VAL A 318 " pdb=" C VAL A 318 " ideal model delta sigma weight residual 112.80 109.72 3.08 1.15e+00 7.56e-01 7.19e+00 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 120.44 123.89 -3.45 1.30e+00 5.92e-01 7.05e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.38 111.77 -3.39 1.35e+00 5.49e-01 6.29e+00 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 119.69 -5.29 2.30e+00 1.89e-01 5.28e+00 angle pdb=" N ILE A 421 " pdb=" CA ILE A 421 " pdb=" C ILE A 421 " ideal model delta sigma weight residual 112.98 110.18 2.80 1.25e+00 6.40e-01 5.03e+00 ... (remaining 9045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3599 17.97 - 35.94: 318 35.94 - 53.91: 53 53.91 - 71.88: 12 71.88 - 89.85: 11 Dihedral angle restraints: 3993 sinusoidal: 1671 harmonic: 2322 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 8.59 84.41 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 15.94 77.06 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 23.03 69.97 1 1.00e+01 1.00e-02 6.31e+01 ... (remaining 3990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 578 0.029 - 0.058: 260 0.058 - 0.087: 72 0.087 - 0.115: 51 0.115 - 0.144: 4 Chirality restraints: 965 Sorted by residual: chirality pdb=" CA PHE C 456 " pdb=" N PHE C 456 " pdb=" C PHE C 456 " pdb=" CB PHE C 456 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE A 468 " pdb=" N ILE A 468 " pdb=" C ILE A 468 " pdb=" CB ILE A 468 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA PRO A 253 " pdb=" N PRO A 253 " pdb=" C PRO A 253 " pdb=" CB PRO A 253 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 962 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 488 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C CYS C 488 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS C 488 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR C 489 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 500 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 583 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.020 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 103 2.66 - 3.22: 6014 3.22 - 3.78: 10236 3.78 - 4.34: 14322 4.34 - 4.90: 23151 Nonbonded interactions: 53826 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.100 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.176 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.236 3.040 nonbonded pdb=" O SER A 254 " pdb=" OG SER A 254 " model vdw 2.241 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.302 3.120 ... (remaining 53821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.230 Find NCS groups from input model: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.004 0.201 6671 Z= 0.189 Angle : 0.576 8.657 9079 Z= 0.315 Chirality : 0.040 0.144 965 Planarity : 0.003 0.036 1165 Dihedral : 14.105 89.849 2484 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.29 % Allowed : 2.73 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.27), residues: 788 helix: -0.20 (0.24), residues: 395 sheet: -2.05 (0.62), residues: 56 loop : -1.70 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.015 0.001 TYR A 381 PHE 0.016 0.001 PHE A 369 TRP 0.011 0.001 TRP A 302 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6657) covalent geometry : angle 0.55504 ( 9050) SS BOND : bond 0.00264 ( 7) SS BOND : angle 2.46969 ( 14) hydrogen bonds : bond 0.14992 ( 310) hydrogen bonds : angle 5.38033 ( 881) metal coordination : bond 0.19010 ( 2) link_NAG-ASN : bond 0.00270 ( 5) link_NAG-ASN : angle 3.05573 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7984 (mmmm) cc_final: 0.7258 (pttt) REVERT: A 195 HIS cc_start: 0.8245 (m90) cc_final: 0.8042 (m170) REVERT: A 202 TYR cc_start: 0.7367 (t80) cc_final: 0.7158 (t80) REVERT: A 474 MET cc_start: 0.7289 (mmp) cc_final: 0.6873 (mmt) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.0863 time to fit residues: 14.5095 Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.0030 overall best weight: 2.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 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 = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118637 restraints weight = 8815.258| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.11 r_work: 0.3116 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6671 Z= 0.187 Angle : 0.608 8.079 9079 Z= 0.306 Chirality : 0.043 0.147 965 Planarity : 0.004 0.047 1165 Dihedral : 5.277 56.819 967 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.73 % Allowed : 10.94 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 788 helix: 0.58 (0.25), residues: 401 sheet: -1.71 (0.61), residues: 60 loop : -1.26 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 482 TYR 0.028 0.002 TYR A 381 PHE 0.019 0.002 PHE A 369 TRP 0.015 0.002 TRP A 302 HIS 0.004 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6657) covalent geometry : angle 0.58752 ( 9050) SS BOND : bond 0.00329 ( 7) SS BOND : angle 2.73318 ( 14) hydrogen bonds : bond 0.05025 ( 310) hydrogen bonds : angle 4.52769 ( 881) metal coordination : bond 0.01269 ( 2) link_NAG-ASN : bond 0.00299 ( 5) link_NAG-ASN : angle 2.90818 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8138 (mmmm) cc_final: 0.7184 (pttt) REVERT: A 474 MET cc_start: 0.7610 (mmp) cc_final: 0.7069 (mmp) REVERT: C 378 LYS cc_start: 0.6710 (mtpt) cc_final: 0.5861 (ptmm) REVERT: C 492 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6989 (mp) outliers start: 12 outliers final: 6 residues processed: 109 average time/residue: 0.0738 time to fit residues: 10.8599 Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124201 restraints weight = 15877.907| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.91 r_work: 0.3034 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6671 Z= 0.125 Angle : 0.552 6.911 9079 Z= 0.276 Chirality : 0.041 0.135 965 Planarity : 0.003 0.028 1165 Dihedral : 4.808 52.911 967 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.01 % Allowed : 13.09 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 788 helix: 1.07 (0.26), residues: 402 sheet: -1.49 (0.65), residues: 58 loop : -0.95 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.016 0.001 TYR A 381 PHE 0.017 0.001 PHE A 369 TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6657) covalent geometry : angle 0.53475 ( 9050) SS BOND : bond 0.00360 ( 7) SS BOND : angle 2.47175 ( 14) hydrogen bonds : bond 0.04366 ( 310) hydrogen bonds : angle 4.33021 ( 881) metal coordination : bond 0.00307 ( 2) link_NAG-ASN : bond 0.00244 ( 5) link_NAG-ASN : angle 2.52019 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7168 (pttt) REVERT: A 474 MET cc_start: 0.7602 (mmp) cc_final: 0.7021 (mmp) REVERT: A 495 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7287 (mm-30) REVERT: C 378 LYS cc_start: 0.6759 (mtpt) cc_final: 0.5787 (ptmm) REVERT: C 452 LEU cc_start: 0.7914 (mp) cc_final: 0.7614 (mm) REVERT: C 492 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7028 (mp) outliers start: 14 outliers final: 11 residues processed: 110 average time/residue: 0.0834 time to fit residues: 12.2050 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119513 restraints weight = 11253.746| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.33 r_work: 0.3087 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6671 Z= 0.145 Angle : 0.566 6.699 9079 Z= 0.284 Chirality : 0.041 0.131 965 Planarity : 0.004 0.032 1165 Dihedral : 4.823 47.385 967 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.59 % Allowed : 14.82 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.30), residues: 788 helix: 1.18 (0.26), residues: 401 sheet: -1.50 (0.67), residues: 62 loop : -0.69 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 482 TYR 0.020 0.001 TYR A 381 PHE 0.017 0.001 PHE A 369 TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6657) covalent geometry : angle 0.54987 ( 9050) SS BOND : bond 0.00312 ( 7) SS BOND : angle 2.41511 ( 14) hydrogen bonds : bond 0.04569 ( 310) hydrogen bonds : angle 4.35637 ( 881) metal coordination : bond 0.00382 ( 2) link_NAG-ASN : bond 0.00224 ( 5) link_NAG-ASN : angle 2.47666 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.237 Fit side-chains REVERT: A 114 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7226 (pttt) REVERT: A 190 MET cc_start: 0.7640 (ttt) cc_final: 0.7295 (ttp) REVERT: A 474 MET cc_start: 0.7598 (mmp) cc_final: 0.6975 (mmp) REVERT: C 378 LYS cc_start: 0.6768 (mtpt) cc_final: 0.5804 (ptmm) REVERT: C 409 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: C 452 LEU cc_start: 0.7934 (mp) cc_final: 0.7655 (mm) REVERT: C 492 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7001 (mp) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 0.0747 time to fit residues: 11.0380 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 121 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.156278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123590 restraints weight = 12919.485| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.40 r_work: 0.3130 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6671 Z= 0.106 Angle : 0.522 7.030 9079 Z= 0.262 Chirality : 0.040 0.132 965 Planarity : 0.003 0.025 1165 Dihedral : 4.370 42.791 967 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.30 % Allowed : 15.25 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.30), residues: 788 helix: 1.49 (0.26), residues: 400 sheet: -1.58 (0.67), residues: 60 loop : -0.45 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 482 TYR 0.009 0.001 TYR A 381 PHE 0.016 0.001 PHE A 315 TRP 0.010 0.001 TRP A 477 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6657) covalent geometry : angle 0.50710 ( 9050) SS BOND : bond 0.00286 ( 7) SS BOND : angle 2.26358 ( 14) hydrogen bonds : bond 0.03961 ( 310) hydrogen bonds : angle 4.24206 ( 881) metal coordination : bond 0.00182 ( 2) link_NAG-ASN : bond 0.00218 ( 5) link_NAG-ASN : angle 2.22378 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.287 Fit side-chains REVERT: A 114 LYS cc_start: 0.8058 (mmmm) cc_final: 0.7186 (pttt) REVERT: A 121 ASN cc_start: 0.8103 (m-40) cc_final: 0.7773 (m-40) REVERT: A 198 ASP cc_start: 0.7603 (p0) cc_final: 0.7331 (p0) REVERT: A 474 MET cc_start: 0.7593 (mmp) cc_final: 0.6958 (mmp) REVERT: C 378 LYS cc_start: 0.6694 (mtpt) cc_final: 0.6263 (ptmm) REVERT: C 391 CYS cc_start: 0.5039 (OUTLIER) cc_final: 0.4676 (t) REVERT: C 409 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: C 452 LEU cc_start: 0.7849 (mp) cc_final: 0.7548 (mm) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.0739 time to fit residues: 11.3570 Evaluate side-chains 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120692 restraints weight = 10900.950| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.12 r_work: 0.3084 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6671 Z= 0.156 Angle : 0.575 8.145 9079 Z= 0.287 Chirality : 0.041 0.132 965 Planarity : 0.003 0.029 1165 Dihedral : 4.755 39.921 967 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.73 % Allowed : 15.25 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.30), residues: 788 helix: 1.34 (0.26), residues: 401 sheet: -1.49 (0.67), residues: 62 loop : -0.47 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 482 TYR 0.020 0.001 TYR A 381 PHE 0.016 0.002 PHE A 369 TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6657) covalent geometry : angle 0.55940 ( 9050) SS BOND : bond 0.00284 ( 7) SS BOND : angle 2.30998 ( 14) hydrogen bonds : bond 0.04659 ( 310) hydrogen bonds : angle 4.34266 ( 881) metal coordination : bond 0.00406 ( 2) link_NAG-ASN : bond 0.00470 ( 5) link_NAG-ASN : angle 2.48684 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.220 Fit side-chains REVERT: A 114 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7267 (pttt) REVERT: C 378 LYS cc_start: 0.6895 (mtpt) cc_final: 0.6166 (ptmm) REVERT: C 391 CYS cc_start: 0.5055 (OUTLIER) cc_final: 0.4701 (t) outliers start: 19 outliers final: 15 residues processed: 108 average time/residue: 0.0756 time to fit residues: 11.1355 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.122144 restraints weight = 15890.406| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.67 r_work: 0.3012 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6671 Z= 0.152 Angle : 0.569 6.854 9079 Z= 0.286 Chirality : 0.041 0.131 965 Planarity : 0.004 0.034 1165 Dihedral : 4.654 36.035 967 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.30 % Allowed : 16.12 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.30), residues: 788 helix: 1.32 (0.26), residues: 401 sheet: -1.61 (0.67), residues: 60 loop : -0.45 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 482 TYR 0.019 0.001 TYR A 381 PHE 0.015 0.002 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6657) covalent geometry : angle 0.55412 ( 9050) SS BOND : bond 0.00306 ( 7) SS BOND : angle 2.28290 ( 14) hydrogen bonds : bond 0.04630 ( 310) hydrogen bonds : angle 4.35407 ( 881) metal coordination : bond 0.00419 ( 2) link_NAG-ASN : bond 0.00163 ( 5) link_NAG-ASN : angle 2.37397 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.221 Fit side-chains REVERT: A 114 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7257 (pttt) REVERT: C 378 LYS cc_start: 0.6954 (mtpt) cc_final: 0.6063 (ptmm) REVERT: C 391 CYS cc_start: 0.4985 (OUTLIER) cc_final: 0.4534 (t) REVERT: C 409 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.7296 (mp10) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.0665 time to fit residues: 9.4614 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.156118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125384 restraints weight = 15855.505| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.78 r_work: 0.3052 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6671 Z= 0.106 Angle : 0.522 7.432 9079 Z= 0.263 Chirality : 0.040 0.125 965 Planarity : 0.003 0.024 1165 Dihedral : 4.134 33.969 965 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.87 % Allowed : 16.55 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.30), residues: 788 helix: 1.60 (0.26), residues: 399 sheet: -1.25 (0.73), residues: 50 loop : -0.34 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 482 TYR 0.008 0.001 TYR A 381 PHE 0.015 0.001 PHE A 315 TRP 0.010 0.001 TRP A 163 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6657) covalent geometry : angle 0.51003 ( 9050) SS BOND : bond 0.00320 ( 7) SS BOND : angle 2.09041 ( 14) hydrogen bonds : bond 0.03965 ( 310) hydrogen bonds : angle 4.22209 ( 881) metal coordination : bond 0.00220 ( 2) link_NAG-ASN : bond 0.00179 ( 5) link_NAG-ASN : angle 2.04491 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.237 Fit side-chains REVERT: A 114 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7235 (pttt) REVERT: A 215 TYR cc_start: 0.8236 (m-80) cc_final: 0.7951 (m-10) REVERT: A 474 MET cc_start: 0.7662 (mmp) cc_final: 0.6946 (mmp) REVERT: C 378 LYS cc_start: 0.6861 (mtpt) cc_final: 0.6437 (ptmm) REVERT: C 409 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: C 452 LEU cc_start: 0.7858 (mp) cc_final: 0.7537 (mm) outliers start: 13 outliers final: 12 residues processed: 113 average time/residue: 0.0750 time to fit residues: 11.4191 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 0.0270 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.156430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125066 restraints weight = 10912.948| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.19 r_work: 0.3161 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6671 Z= 0.107 Angle : 0.528 7.462 9079 Z= 0.265 Chirality : 0.040 0.127 965 Planarity : 0.003 0.033 1165 Dihedral : 4.023 31.098 965 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.30 % Allowed : 16.83 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.30), residues: 788 helix: 1.66 (0.26), residues: 401 sheet: -1.17 (0.72), residues: 50 loop : -0.29 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 482 TYR 0.009 0.001 TYR A 381 PHE 0.013 0.001 PHE A 315 TRP 0.013 0.001 TRP A 477 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6657) covalent geometry : angle 0.51706 ( 9050) SS BOND : bond 0.00253 ( 7) SS BOND : angle 2.01322 ( 14) hydrogen bonds : bond 0.03956 ( 310) hydrogen bonds : angle 4.19156 ( 881) metal coordination : bond 0.00183 ( 2) link_NAG-ASN : bond 0.00175 ( 5) link_NAG-ASN : angle 1.97519 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.238 Fit side-chains REVERT: A 114 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7262 (pttt) REVERT: A 215 TYR cc_start: 0.8224 (m-80) cc_final: 0.7936 (m-10) REVERT: A 474 MET cc_start: 0.7663 (mmp) cc_final: 0.6940 (mmp) REVERT: C 378 LYS cc_start: 0.6749 (mtpt) cc_final: 0.6268 (ptmm) REVERT: C 391 CYS cc_start: 0.5016 (OUTLIER) cc_final: 0.4504 (t) REVERT: C 409 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.7409 (mp10) outliers start: 16 outliers final: 14 residues processed: 110 average time/residue: 0.0809 time to fit residues: 11.8759 Evaluate side-chains 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 24 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.157261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126324 restraints weight = 17071.174| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.16 r_work: 0.3035 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6671 Z= 0.104 Angle : 0.528 7.456 9079 Z= 0.265 Chirality : 0.040 0.128 965 Planarity : 0.003 0.028 1165 Dihedral : 3.883 28.941 965 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.16 % Allowed : 16.83 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.30), residues: 788 helix: 1.77 (0.26), residues: 399 sheet: -1.06 (0.73), residues: 50 loop : -0.16 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 482 TYR 0.008 0.001 TYR A 516 PHE 0.013 0.001 PHE A 315 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6657) covalent geometry : angle 0.51734 ( 9050) SS BOND : bond 0.00234 ( 7) SS BOND : angle 1.93746 ( 14) hydrogen bonds : bond 0.03840 ( 310) hydrogen bonds : angle 4.16361 ( 881) metal coordination : bond 0.00151 ( 2) link_NAG-ASN : bond 0.00183 ( 5) link_NAG-ASN : angle 1.87516 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.240 Fit side-chains REVERT: A 114 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7227 (pttt) REVERT: A 215 TYR cc_start: 0.8184 (m-80) cc_final: 0.7922 (m-10) REVERT: A 474 MET cc_start: 0.7650 (mmp) cc_final: 0.6998 (mmp) REVERT: A 557 MET cc_start: 0.8780 (tmm) cc_final: 0.8540 (tmm) REVERT: A 607 SER cc_start: 0.7619 (m) cc_final: 0.7125 (p) REVERT: C 378 LYS cc_start: 0.6666 (mtpt) cc_final: 0.6224 (ptmm) REVERT: C 391 CYS cc_start: 0.4974 (OUTLIER) cc_final: 0.4421 (t) REVERT: C 409 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7422 (mp10) outliers start: 15 outliers final: 13 residues processed: 109 average time/residue: 0.0773 time to fit residues: 11.5038 Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.156491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.125422 restraints weight = 17052.231| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.16 r_work: 0.3014 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6671 Z= 0.114 Angle : 0.538 8.872 9079 Z= 0.268 Chirality : 0.040 0.128 965 Planarity : 0.003 0.027 1165 Dihedral : 3.894 26.673 965 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.16 % Allowed : 16.98 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.30), residues: 788 helix: 1.73 (0.26), residues: 401 sheet: -1.03 (0.73), residues: 50 loop : -0.19 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 482 TYR 0.013 0.001 TYR A 50 PHE 0.013 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6657) covalent geometry : angle 0.52807 ( 9050) SS BOND : bond 0.00239 ( 7) SS BOND : angle 1.93880 ( 14) hydrogen bonds : bond 0.04022 ( 310) hydrogen bonds : angle 4.16276 ( 881) metal coordination : bond 0.00218 ( 2) link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 1.89941 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.72 seconds wall clock time: 30 minutes 5.20 seconds (1805.20 seconds total)