Starting phenix.real_space_refine on Tue Mar 11 16:46:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ddp_30653/03_2025/7ddp_30653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ddp_30653/03_2025/7ddp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ddp_30653/03_2025/7ddp_30653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ddp_30653/03_2025/7ddp_30653.map" model { file = "/net/cci-nas-00/data/ceres_data/7ddp_30653/03_2025/7ddp_30653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ddp_30653/03_2025/7ddp_30653.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.07, per 1000 atoms: 0.94 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: 1.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.66 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: 1.61 Time building geometry restraints manager: 1.85 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: 0.200 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.920 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- 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 : 0.003 0.037 6657 Z= 0.186 Angle : 0.555 7.087 9050 Z= 0.310 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 (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: -1.50 (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 TRP 0.011 0.001 TRP A 302 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE A 369 TYR 0.015 0.001 TYR A 381 ARG 0.002 0.000 ARG A 357 *********************** 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 : 0.733 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7258 (pttt) REVERT: A 195 HIS cc_start: 0.8245 (m90) cc_final: 0.8040 (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: 0.6871 (mmt) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.1948 time to fit residues: 32.7971 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 : 0.754 ------------------------------------------------------------------------------- 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 65 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.151758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.120395 restraints weight = 17332.297| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.01 r_work: 0.2958 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 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 = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6657 Z= 0.278 Angle : 0.599 7.004 9050 Z= 0.305 Chirality : 0.043 0.150 965 Planarity : 0.004 0.052 1165 Dihedral : 5.307 56.208 967 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.73 % Allowed : 11.08 % Favored : 87.19 % 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: -0.56 (0.28), residues: 788 helix: 0.58 (0.25), residues: 401 sheet: -1.69 (0.61), residues: 60 loop : -1.24 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 302 HIS 0.004 0.001 HIS A 378 PHE 0.018 0.002 PHE A 369 TYR 0.030 0.002 TYR A 381 ARG 0.003 0.001 ARG A 482 *********************** 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7180 (pttt) REVERT: A 474 MET cc_start: 0.7615 (mmp) cc_final: 0.7058 (mmp) REVERT: A 495 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7220 (mm-30) REVERT: C 378 LYS cc_start: 0.6806 (mtpt) cc_final: 0.5882 (ptmm) REVERT: C 492 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7018 (mp) outliers start: 12 outliers final: 6 residues processed: 108 average time/residue: 0.1771 time to fit residues: 25.9617 Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 62 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 373 HIS ** 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 = 0.3686 r_free = 0.3686 target = 0.153275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121523 restraints weight = 10777.704| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.18 r_work: 0.3101 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6657 Z= 0.198 Angle : 0.544 6.683 9050 Z= 0.276 Chirality : 0.041 0.136 965 Planarity : 0.004 0.032 1165 Dihedral : 4.917 51.077 967 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 13.53 % Favored : 84.32 % 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: -0.01 (0.29), residues: 788 helix: 1.03 (0.26), residues: 402 sheet: -1.67 (0.64), residues: 60 loop : -0.92 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.018 0.001 PHE A 369 TYR 0.018 0.001 TYR A 381 ARG 0.003 0.000 ARG A 460 *********************** 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 114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7222 (pttt) REVERT: A 190 MET cc_start: 0.8013 (ttt) cc_final: 0.7549 (ttp) REVERT: A 474 MET cc_start: 0.7630 (mmp) cc_final: 0.7100 (mmp) REVERT: A 495 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7285 (mm-30) REVERT: C 378 LYS cc_start: 0.6778 (mtpt) cc_final: 0.5838 (ptmm) REVERT: C 452 LEU cc_start: 0.7988 (mp) cc_final: 0.7677 (mm) REVERT: C 492 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7104 (mp) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.1873 time to fit residues: 27.3398 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 504 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.153093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122480 restraints weight = 15911.139| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.58 r_work: 0.3020 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 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 = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6657 Z= 0.200 Angle : 0.545 6.809 9050 Z= 0.278 Chirality : 0.041 0.129 965 Planarity : 0.004 0.032 1165 Dihedral : 4.771 45.102 967 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.30 % Allowed : 15.11 % 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 (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: 0.27 (0.30), residues: 788 helix: 1.22 (0.26), residues: 401 sheet: -1.67 (0.66), residues: 60 loop : -0.71 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.001 PHE A 369 TYR 0.017 0.001 TYR A 381 ARG 0.004 0.000 ARG A 460 *********************** 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8087 (mmmm) cc_final: 0.7192 (pttt) REVERT: C 378 LYS cc_start: 0.6797 (mtpt) cc_final: 0.6117 (ptmm) REVERT: C 409 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: C 452 LEU cc_start: 0.7938 (mp) cc_final: 0.7641 (mm) REVERT: C 492 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7038 (mp) outliers start: 16 outliers final: 11 residues processed: 107 average time/residue: 0.1776 time to fit residues: 25.9290 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.154871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121706 restraints weight = 12821.562| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.45 r_work: 0.3089 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6657 Z= 0.162 Angle : 0.520 7.007 9050 Z= 0.264 Chirality : 0.040 0.128 965 Planarity : 0.003 0.027 1165 Dihedral : 4.485 40.745 967 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.59 % Allowed : 15.25 % Favored : 82.16 % 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: 0.50 (0.30), residues: 788 helix: 1.39 (0.26), residues: 402 sheet: -1.63 (0.67), residues: 60 loop : -0.56 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.014 0.001 PHE A 369 TYR 0.012 0.001 TYR A 381 ARG 0.004 0.000 ARG A 460 *********************** 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 115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8070 (mmmm) cc_final: 0.7205 (pttt) REVERT: C 378 LYS cc_start: 0.6822 (mtpt) cc_final: 0.6194 (ptmm) REVERT: C 391 CYS cc_start: 0.4992 (OUTLIER) cc_final: 0.4626 (t) REVERT: C 409 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: C 452 LEU cc_start: 0.7890 (mp) cc_final: 0.7585 (mm) outliers start: 18 outliers final: 16 residues processed: 109 average time/residue: 0.1784 time to fit residues: 26.4989 Evaluate side-chains 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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 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 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 27 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN 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 = 0.3679 r_free = 0.3679 target = 0.152518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118974 restraints weight = 8719.790| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.08 r_work: 0.3113 rms_B_bonded: 2.72 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: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6657 Z= 0.232 Angle : 0.564 8.627 9050 Z= 0.284 Chirality : 0.041 0.129 965 Planarity : 0.004 0.035 1165 Dihedral : 4.739 37.267 967 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.88 % Allowed : 15.83 % Favored : 81.29 % 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: 0.39 (0.30), residues: 788 helix: 1.26 (0.26), residues: 401 sheet: -1.56 (0.67), residues: 62 loop : -0.56 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.002 PHE A 369 TYR 0.019 0.001 TYR A 381 ARG 0.005 0.000 ARG A 460 *********************** 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 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7272 (pttt) REVERT: C 378 LYS cc_start: 0.7034 (mtpt) cc_final: 0.6201 (ptmm) REVERT: C 391 CYS cc_start: 0.5049 (OUTLIER) cc_final: 0.4660 (t) REVERT: C 409 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.7307 (mp10) outliers start: 20 outliers final: 15 residues processed: 104 average time/residue: 0.1784 time to fit residues: 25.2293 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 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 47 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 73 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.156225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124511 restraints weight = 10777.176| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.27 r_work: 0.3168 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 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 = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6657 Z= 0.137 Angle : 0.506 7.389 9050 Z= 0.255 Chirality : 0.040 0.127 965 Planarity : 0.003 0.026 1165 Dihedral : 4.227 33.870 967 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.59 % Allowed : 16.83 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.30), residues: 788 helix: 1.60 (0.26), residues: 399 sheet: -1.57 (0.67), residues: 60 loop : -0.36 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.007 0.001 HIS A 374 PHE 0.014 0.001 PHE A 315 TYR 0.008 0.001 TYR A 50 ARG 0.002 0.000 ARG A 460 *********************** 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 118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8135 (mmmm) cc_final: 0.7251 (pttt) REVERT: C 378 LYS cc_start: 0.6867 (mtpt) cc_final: 0.6365 (ptmm) REVERT: C 391 CYS cc_start: 0.4939 (OUTLIER) cc_final: 0.4452 (t) REVERT: C 409 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7402 (mp10) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.1827 time to fit residues: 27.3910 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.155492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121854 restraints weight = 8690.271| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.10 r_work: 0.3147 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 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 = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6657 Z= 0.162 Angle : 0.517 7.260 9050 Z= 0.261 Chirality : 0.040 0.126 965 Planarity : 0.003 0.028 1165 Dihedral : 4.229 32.605 967 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.45 % Allowed : 16.83 % Favored : 80.72 % 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: 0.82 (0.30), residues: 788 helix: 1.59 (0.26), residues: 401 sheet: -1.47 (0.67), residues: 60 loop : -0.29 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.014 0.001 PHE A 369 TYR 0.012 0.001 TYR A 381 ARG 0.010 0.000 ARG A 482 *********************** 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 115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.647 Fit side-chains REVERT: A 114 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7233 (pttt) REVERT: C 378 LYS cc_start: 0.6821 (mtpt) cc_final: 0.6314 (ptmm) REVERT: C 391 CYS cc_start: 0.4933 (OUTLIER) cc_final: 0.4453 (t) REVERT: C 409 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7322 (mp10) outliers start: 17 outliers final: 15 residues processed: 109 average time/residue: 0.1898 time to fit residues: 27.7470 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 132 VAL 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 504 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 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 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 = 0.3718 r_free = 0.3718 target = 0.156094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125502 restraints weight = 8806.515| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.02 r_work: 0.3187 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6657 Z= 0.162 Angle : 0.514 7.382 9050 Z= 0.260 Chirality : 0.040 0.125 965 Planarity : 0.003 0.026 1165 Dihedral : 4.056 31.291 965 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.45 % Allowed : 16.98 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.30), residues: 788 helix: 1.60 (0.26), residues: 401 sheet: -1.12 (0.73), residues: 50 loop : -0.29 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.017 0.001 PHE A 315 TYR 0.010 0.001 TYR A 381 ARG 0.010 0.000 ARG A 482 *********************** 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 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8135 (mmmm) cc_final: 0.7256 (pttt) REVERT: A 215 TYR cc_start: 0.8212 (m-80) cc_final: 0.7950 (m-10) REVERT: C 378 LYS cc_start: 0.6749 (mtpt) cc_final: 0.6294 (ptmm) REVERT: C 391 CYS cc_start: 0.4995 (OUTLIER) cc_final: 0.4524 (t) REVERT: C 409 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.7342 (mp10) outliers start: 17 outliers final: 15 residues processed: 110 average time/residue: 0.1710 time to fit residues: 25.6599 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 132 VAL 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 504 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0670 chunk 23 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.156731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123464 restraints weight = 12867.976| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.48 r_work: 0.3108 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 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 = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6657 Z= 0.153 Angle : 0.518 7.451 9050 Z= 0.262 Chirality : 0.040 0.126 965 Planarity : 0.003 0.027 1165 Dihedral : 3.970 29.862 965 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.45 % Allowed : 17.27 % Favored : 80.29 % 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: 0.99 (0.30), residues: 788 helix: 1.66 (0.26), residues: 401 sheet: -1.05 (0.73), residues: 50 loop : -0.23 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.006 0.001 HIS A 374 PHE 0.017 0.001 PHE A 315 TYR 0.008 0.001 TYR A 381 ARG 0.010 0.000 ARG A 482 ********************** 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 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8097 (mmmm) cc_final: 0.7228 (pttt) REVERT: A 215 TYR cc_start: 0.8153 (m-80) cc_final: 0.7892 (m-10) REVERT: C 378 LYS cc_start: 0.6693 (mtpt) cc_final: 0.6259 (ptmm) REVERT: C 391 CYS cc_start: 0.4967 (OUTLIER) cc_final: 0.4476 (t) REVERT: C 409 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.7304 (mp10) outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.1997 time to fit residues: 29.6694 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 504 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.0060 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.0070 chunk 55 optimal weight: 0.8980 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.160790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128924 restraints weight = 11301.847| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.31 r_work: 0.3183 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6657 Z= 0.128 Angle : 0.500 7.605 9050 Z= 0.252 Chirality : 0.039 0.126 965 Planarity : 0.003 0.026 1165 Dihedral : 3.654 25.864 965 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.16 % Allowed : 17.70 % Favored : 80.14 % 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: 1.22 (0.31), residues: 788 helix: 1.85 (0.26), residues: 399 sheet: -0.96 (0.73), residues: 50 loop : -0.11 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.008 0.001 HIS A 374 PHE 0.017 0.001 PHE A 315 TYR 0.008 0.001 TYR A 516 ARG 0.009 0.000 ARG A 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3964.85 seconds wall clock time: 68 minutes 50.12 seconds (4130.12 seconds total)