Starting phenix.real_space_refine on Mon Apr 28 15:16:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxw_38763/04_2025/8xxw_38763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxw_38763/04_2025/8xxw_38763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxw_38763/04_2025/8xxw_38763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxw_38763/04_2025/8xxw_38763.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxw_38763/04_2025/8xxw_38763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxw_38763/04_2025/8xxw_38763.cif" } resolution = 3.03 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= 0.001 sd= 0.018 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 41 5.16 5 C 4932 2.51 5 N 1278 2.21 5 O 1471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7723 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 561, 4588 Classifications: {'peptide': 561} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 537} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 561, 4588 Classifications: {'peptide': 561} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 537} Chain breaks: 2 bond proxies already assigned to first conformer: 4703 Chain: "E" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1300 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain breaks: 2 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 845 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: 7.97, per 1000 atoms: 1.03 Number of scatterers: 7723 At special positions: 0 Unit cell: (70.55, 86.7, 141.1, 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 41 16.00 O 1471 8.00 N 1278 7.00 C 4932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 E 701 " - " ASN E 343 " Time building additional restraints: 2.55 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 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 50.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.590A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 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: 4.021A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.891A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.989A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 127 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 193 removed outlier: 3.747A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.161A 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 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 219 through 252 removed outlier: 4.157A 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 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.690A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.735A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.975A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.740A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (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 448 through 466 removed outlier: 4.245A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.478A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.723A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.837A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.932A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.607A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.712A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.586A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.944A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 104 removed outlier: 3.570A pdb=" N GLY H 103 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.593A pdb=" N MET L 83 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.039A 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 352 removed outlier: 6.129A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.579A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.482A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2473 1.34 - 1.46: 1947 1.46 - 1.58: 3437 1.58 - 1.69: 1 1.69 - 1.81: 67 Bond restraints: 7925 Sorted by residual: bond pdb=" C LEU A 262 " pdb=" N PRO A 263 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.31e-02 5.83e+03 4.99e+00 bond pdb=" N ASP E 428 " pdb=" CA ASP E 428 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.31e-02 5.83e+03 4.27e+00 bond pdb=" N LEU A 262 " pdb=" CA LEU A 262 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.41e-02 5.03e+03 2.93e+00 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " 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 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.81e+00 ... (remaining 7920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 10421 1.36 - 2.72: 241 2.72 - 4.07: 63 4.07 - 5.43: 18 5.43 - 6.79: 4 Bond angle restraints: 10747 Sorted by residual: angle pdb=" O CYS A 261 " pdb=" C CYS A 261 " pdb=" N LEU A 262 " ideal model delta sigma weight residual 123.10 127.10 -4.00 1.15e+00 7.56e-01 1.21e+01 angle pdb=" N GLY H 103 " pdb=" CA GLY H 103 " pdb=" C GLY H 103 " ideal model delta sigma weight residual 115.46 110.53 4.93 1.63e+00 3.76e-01 9.14e+00 angle pdb=" CA MET A 270 " pdb=" CB MET A 270 " pdb=" CG MET A 270 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.71e+00 angle pdb=" CA PRO A 500 " pdb=" N PRO A 500 " pdb=" CD PRO A 500 " ideal model delta sigma weight residual 112.00 107.93 4.07 1.40e+00 5.10e-01 8.46e+00 angle pdb=" CA CYS A 261 " pdb=" C CYS A 261 " pdb=" N LEU A 262 " ideal model delta sigma weight residual 115.55 111.87 3.68 1.33e+00 5.65e-01 7.67e+00 ... (remaining 10742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 4085 17.19 - 34.37: 453 34.37 - 51.56: 137 51.56 - 68.75: 26 68.75 - 85.94: 9 Dihedral angle restraints: 4710 sinusoidal: 1935 harmonic: 2775 Sorted by residual: dihedral pdb=" CA ASP A 597 " pdb=" CB ASP A 597 " pdb=" CG ASP A 597 " pdb=" OD1 ASP A 597 " ideal model delta sinusoidal sigma weight residual -30.00 -87.84 57.84 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA TYR H 60 " pdb=" C TYR H 60 " pdb=" N ASP H 61 " pdb=" CA ASP H 61 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -59.17 -26.83 1 1.00e+01 1.00e-02 1.03e+01 ... (remaining 4707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 791 0.038 - 0.076: 247 0.076 - 0.114: 82 0.114 - 0.152: 11 0.152 - 0.190: 1 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CA LEU A 262 " pdb=" N LEU A 262 " pdb=" C LEU A 262 " pdb=" CB LEU A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA ARG A 192 " pdb=" N ARG A 192 " pdb=" C ARG A 192 " pdb=" CB ARG A 192 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA PRO A 500 " pdb=" N PRO A 500 " pdb=" C PRO A 500 " pdb=" CB PRO A 500 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 1129 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.057 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO A 500 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 61 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO H 62 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO H 62 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 62 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 52 " 0.039 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO H 53 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " 0.033 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 817 2.75 - 3.29: 7301 3.29 - 3.82: 12512 3.82 - 4.36: 14663 4.36 - 4.90: 25812 Nonbonded interactions: 61105 Sorted by model distance: nonbonded pdb=" OD1 ASP A 269 " pdb=" N GLY A 272 " model vdw 2.212 3.120 nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 279 " pdb=" OD1 ASN A 290 " model vdw 2.262 3.040 nonbonded pdb=" N GLU A 430 " pdb=" OE1 GLU A 430 " model vdw 2.296 3.120 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 116 " model vdw 2.303 3.040 ... (remaining 61100 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=0.24 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: 391.130 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 421.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 0.052 7936 Z= 0.143 Angle : 0.569 6.790 10768 Z= 0.306 Chirality : 0.041 0.190 1132 Planarity : 0.005 0.084 1385 Dihedral : 16.104 85.937 2918 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.12 % Allowed : 19.42 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.00 (0.28), residues: 935 helix: 1.22 (0.27), residues: 390 sheet: 0.91 (0.39), residues: 179 loop : 0.07 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 566 HIS 0.003 0.001 HIS A 540 PHE 0.029 0.001 PHE A 504 TYR 0.012 0.001 TYR A 50 ARG 0.003 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00049 ( 3) link_NAG-ASN : angle 1.38433 ( 9) hydrogen bonds : bond 0.15791 ( 376) hydrogen bonds : angle 6.07891 ( 1028) metal coordination : bond 0.00096 ( 2) SS BOND : bond 0.00334 ( 6) SS BOND : angle 0.60067 ( 12) covalent geometry : bond 0.00296 ( 7925) covalent geometry : angle 0.56747 (10747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8402 (mp10) cc_final: 0.8155 (mp10) REVERT: E 443 SER cc_start: 0.8660 (m) cc_final: 0.8331 (p) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2394 time to fit residues: 48.2194 Evaluate side-chains 153 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.0040 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 0.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 63 ASN E 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111718 restraints weight = 10885.743| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.07 r_work: 0.3293 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7936 Z= 0.123 Angle : 0.517 8.497 10768 Z= 0.270 Chirality : 0.041 0.129 1132 Planarity : 0.005 0.062 1385 Dihedral : 4.229 34.448 1099 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.97 % Allowed : 18.58 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.16 (0.27), residues: 935 helix: 1.25 (0.26), residues: 392 sheet: 0.96 (0.39), residues: 181 loop : 0.29 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE H 99 TYR 0.017 0.001 TYR A 243 ARG 0.005 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 3) link_NAG-ASN : angle 1.57554 ( 9) hydrogen bonds : bond 0.05008 ( 376) hydrogen bonds : angle 4.59206 ( 1028) metal coordination : bond 0.00161 ( 2) SS BOND : bond 0.00428 ( 6) SS BOND : angle 0.69908 ( 12) covalent geometry : bond 0.00275 ( 7925) covalent geometry : angle 0.51496 (10747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.853 Fit side-chains REVERT: A 123 MET cc_start: 0.5210 (mmp) cc_final: 0.4552 (mmm) REVERT: A 183 TYR cc_start: 0.7228 (t80) cc_final: 0.6874 (t80) REVERT: E 443 SER cc_start: 0.8617 (m) cc_final: 0.8242 (p) outliers start: 8 outliers final: 4 residues processed: 168 average time/residue: 0.2326 time to fit residues: 50.7856 Evaluate side-chains 174 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain L residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.0000 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.0170 overall best weight: 0.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS E 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111930 restraints weight = 13342.774| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.37 r_work: 0.3285 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7936 Z= 0.106 Angle : 0.492 7.550 10768 Z= 0.255 Chirality : 0.040 0.127 1132 Planarity : 0.004 0.053 1385 Dihedral : 3.947 31.353 1099 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.09 % Allowed : 18.46 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.41 (0.28), residues: 935 helix: 1.38 (0.26), residues: 394 sheet: 1.24 (0.40), residues: 175 loop : 0.43 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.003 0.001 HIS A 374 PHE 0.010 0.001 PHE H 99 TYR 0.018 0.001 TYR A 243 ARG 0.002 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 3) link_NAG-ASN : angle 1.41560 ( 9) hydrogen bonds : bond 0.04482 ( 376) hydrogen bonds : angle 4.36839 ( 1028) metal coordination : bond 0.00109 ( 2) SS BOND : bond 0.00368 ( 6) SS BOND : angle 0.59287 ( 12) covalent geometry : bond 0.00227 ( 7925) covalent geometry : angle 0.49073 (10747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.775 Fit side-chains REVERT: A 123 MET cc_start: 0.5175 (mmp) cc_final: 0.4684 (mmm) REVERT: A 157 ASP cc_start: 0.6490 (p0) cc_final: 0.6128 (p0) REVERT: A 183 TYR cc_start: 0.7248 (t80) cc_final: 0.6953 (t80) REVERT: E 438 SER cc_start: 0.8323 (p) cc_final: 0.8102 (p) REVERT: E 442 ASP cc_start: 0.8398 (m-30) cc_final: 0.8123 (m-30) REVERT: E 443 SER cc_start: 0.8599 (m) cc_final: 0.8151 (p) outliers start: 9 outliers final: 7 residues processed: 173 average time/residue: 0.2135 time to fit residues: 48.5405 Evaluate side-chains 167 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 81 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108036 restraints weight = 20498.706| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.06 r_work: 0.3199 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7936 Z= 0.132 Angle : 0.513 7.291 10768 Z= 0.266 Chirality : 0.041 0.130 1132 Planarity : 0.004 0.050 1385 Dihedral : 3.992 30.646 1099 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.93 % Allowed : 18.34 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.41 (0.28), residues: 935 helix: 1.37 (0.26), residues: 394 sheet: 1.09 (0.40), residues: 177 loop : 0.54 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.001 PHE H 99 TYR 0.017 0.001 TYR A 243 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 3) link_NAG-ASN : angle 1.66996 ( 9) hydrogen bonds : bond 0.05032 ( 376) hydrogen bonds : angle 4.39214 ( 1028) metal coordination : bond 0.00185 ( 2) SS BOND : bond 0.00427 ( 6) SS BOND : angle 0.90691 ( 12) covalent geometry : bond 0.00301 ( 7925) covalent geometry : angle 0.51063 (10747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.761 Fit side-chains REVERT: A 123 MET cc_start: 0.5164 (mmp) cc_final: 0.4765 (mmm) REVERT: E 442 ASP cc_start: 0.8389 (m-30) cc_final: 0.8163 (m-30) REVERT: E 443 SER cc_start: 0.8586 (m) cc_final: 0.8167 (p) outliers start: 16 outliers final: 11 residues processed: 169 average time/residue: 0.2127 time to fit residues: 47.1869 Evaluate side-chains 168 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 90 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109479 restraints weight = 13663.640| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.40 r_work: 0.3246 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7936 Z= 0.139 Angle : 0.522 6.995 10768 Z= 0.271 Chirality : 0.041 0.131 1132 Planarity : 0.004 0.049 1385 Dihedral : 4.012 29.914 1099 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.17 % Allowed : 18.21 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.39 (0.28), residues: 935 helix: 1.36 (0.27), residues: 394 sheet: 1.08 (0.39), residues: 176 loop : 0.54 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE H 99 TYR 0.017 0.001 TYR A 243 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 3) link_NAG-ASN : angle 1.76212 ( 9) hydrogen bonds : bond 0.05095 ( 376) hydrogen bonds : angle 4.39526 ( 1028) metal coordination : bond 0.00209 ( 2) SS BOND : bond 0.00420 ( 6) SS BOND : angle 0.94440 ( 12) covalent geometry : bond 0.00323 ( 7925) covalent geometry : angle 0.51868 (10747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.770 Fit side-chains REVERT: A 123 MET cc_start: 0.5290 (mmp) cc_final: 0.4925 (mmm) REVERT: A 310 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7591 (mm-30) REVERT: A 312 GLU cc_start: 0.8225 (tt0) cc_final: 0.7706 (tt0) REVERT: E 442 ASP cc_start: 0.8489 (m-30) cc_final: 0.8236 (m-30) REVERT: E 443 SER cc_start: 0.8553 (m) cc_final: 0.8134 (p) outliers start: 18 outliers final: 12 residues processed: 174 average time/residue: 0.2211 time to fit residues: 50.6562 Evaluate side-chains 176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain L residue 10 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 66 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106732 restraints weight = 20846.305| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.14 r_work: 0.3177 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7936 Z= 0.151 Angle : 0.530 6.087 10768 Z= 0.277 Chirality : 0.042 0.134 1132 Planarity : 0.004 0.049 1385 Dihedral : 4.072 29.513 1099 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.05 % Allowed : 18.70 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.33 (0.28), residues: 935 helix: 1.33 (0.27), residues: 394 sheet: 1.00 (0.39), residues: 176 loop : 0.49 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.001 PHE H 99 TYR 0.020 0.002 TYR A 279 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 3) link_NAG-ASN : angle 1.88932 ( 9) hydrogen bonds : bond 0.05299 ( 376) hydrogen bonds : angle 4.42850 ( 1028) metal coordination : bond 0.00230 ( 2) SS BOND : bond 0.00448 ( 6) SS BOND : angle 1.04822 ( 12) covalent geometry : bond 0.00352 ( 7925) covalent geometry : angle 0.52640 (10747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.774 Fit side-chains REVERT: A 123 MET cc_start: 0.5419 (mmp) cc_final: 0.5071 (mmm) REVERT: E 442 ASP cc_start: 0.8585 (m-30) cc_final: 0.8258 (m-30) REVERT: E 443 SER cc_start: 0.8562 (m) cc_final: 0.8138 (p) REVERT: L 4 MET cc_start: 0.8032 (mmm) cc_final: 0.7497 (mmm) REVERT: L 19 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7922 (m) outliers start: 17 outliers final: 13 residues processed: 171 average time/residue: 0.2267 time to fit residues: 50.7485 Evaluate side-chains 177 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.0670 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 71 optimal weight: 0.0170 chunk 9 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109383 restraints weight = 13640.805| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.34 r_work: 0.3251 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 7936 Z= 0.122 Angle : 0.524 9.208 10768 Z= 0.270 Chirality : 0.041 0.130 1132 Planarity : 0.004 0.048 1385 Dihedral : 3.938 27.858 1099 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.69 % Allowed : 19.06 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.43 (0.28), residues: 935 helix: 1.42 (0.27), residues: 394 sheet: 1.04 (0.39), residues: 176 loop : 0.54 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE H 99 TYR 0.022 0.001 TYR A 279 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 3) link_NAG-ASN : angle 1.64726 ( 9) hydrogen bonds : bond 0.04735 ( 376) hydrogen bonds : angle 4.36456 ( 1028) metal coordination : bond 0.00158 ( 2) SS BOND : bond 0.00365 ( 6) SS BOND : angle 0.83128 ( 12) covalent geometry : bond 0.00283 ( 7925) covalent geometry : angle 0.52126 (10747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.883 Fit side-chains REVERT: A 123 MET cc_start: 0.5502 (mmp) cc_final: 0.5230 (mmm) REVERT: A 310 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 312 GLU cc_start: 0.8410 (tt0) cc_final: 0.7914 (tt0) REVERT: E 443 SER cc_start: 0.8597 (m) cc_final: 0.8161 (p) outliers start: 14 outliers final: 12 residues processed: 171 average time/residue: 0.2945 time to fit residues: 65.3488 Evaluate side-chains 175 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 11 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106930 restraints weight = 15537.382| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.52 r_work: 0.3206 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 7936 Z= 0.169 Angle : 0.566 9.387 10768 Z= 0.294 Chirality : 0.042 0.140 1132 Planarity : 0.004 0.048 1385 Dihedral : 4.118 28.309 1099 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.41 % Allowed : 18.70 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.27 (0.28), residues: 935 helix: 1.32 (0.27), residues: 392 sheet: 0.97 (0.39), residues: 176 loop : 0.41 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.015 0.001 PHE H 99 TYR 0.022 0.002 TYR A 50 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 3) link_NAG-ASN : angle 1.99904 ( 9) hydrogen bonds : bond 0.05597 ( 376) hydrogen bonds : angle 4.47199 ( 1028) metal coordination : bond 0.00288 ( 2) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.24156 ( 12) covalent geometry : bond 0.00398 ( 7925) covalent geometry : angle 0.56223 (10747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.289 Fit side-chains REVERT: A 123 MET cc_start: 0.5474 (mmp) cc_final: 0.5192 (mmm) REVERT: A 310 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 312 GLU cc_start: 0.8260 (tt0) cc_final: 0.7734 (tt0) REVERT: E 443 SER cc_start: 0.8561 (m) cc_final: 0.8134 (p) REVERT: L 19 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7947 (m) outliers start: 20 outliers final: 13 residues processed: 174 average time/residue: 0.2677 time to fit residues: 62.1117 Evaluate side-chains 175 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106046 restraints weight = 19133.819| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.86 r_work: 0.3177 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 7936 Z= 0.164 Angle : 0.565 9.246 10768 Z= 0.293 Chirality : 0.042 0.140 1132 Planarity : 0.004 0.049 1385 Dihedral : 4.177 28.345 1099 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.29 % Allowed : 19.06 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.21 (0.28), residues: 935 helix: 1.29 (0.27), residues: 392 sheet: 0.80 (0.39), residues: 182 loop : 0.43 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.001 PHE H 99 TYR 0.024 0.002 TYR A 279 ARG 0.004 0.000 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 3) link_NAG-ASN : angle 1.99000 ( 9) hydrogen bonds : bond 0.05442 ( 376) hydrogen bonds : angle 4.49743 ( 1028) metal coordination : bond 0.00268 ( 2) SS BOND : bond 0.00423 ( 6) SS BOND : angle 1.22692 ( 12) covalent geometry : bond 0.00390 ( 7925) covalent geometry : angle 0.56115 (10747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.868 Fit side-chains REVERT: A 123 MET cc_start: 0.5565 (mmp) cc_final: 0.5280 (mmm) REVERT: A 310 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 312 GLU cc_start: 0.8304 (tt0) cc_final: 0.7783 (tt0) REVERT: A 518 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7671 (mtp-110) REVERT: E 442 ASP cc_start: 0.8485 (m-30) cc_final: 0.8215 (m-30) REVERT: E 443 SER cc_start: 0.8573 (m) cc_final: 0.8165 (p) REVERT: L 19 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7947 (m) outliers start: 19 outliers final: 12 residues processed: 174 average time/residue: 0.2085 time to fit residues: 47.8732 Evaluate side-chains 176 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 18 optimal weight: 0.3980 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.0070 chunk 78 optimal weight: 0.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 239 HIS A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107149 restraints weight = 20810.885| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.02 r_work: 0.3190 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 7936 Z= 0.127 Angle : 0.537 8.919 10768 Z= 0.280 Chirality : 0.041 0.147 1132 Planarity : 0.004 0.048 1385 Dihedral : 3.989 27.088 1099 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.57 % Allowed : 19.90 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.36 (0.28), residues: 935 helix: 1.35 (0.27), residues: 392 sheet: 1.22 (0.40), residues: 166 loop : 0.42 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE H 99 TYR 0.020 0.001 TYR A 243 ARG 0.003 0.000 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 3) link_NAG-ASN : angle 1.72208 ( 9) hydrogen bonds : bond 0.04864 ( 376) hydrogen bonds : angle 4.41111 ( 1028) metal coordination : bond 0.00171 ( 2) SS BOND : bond 0.00402 ( 6) SS BOND : angle 0.79108 ( 12) covalent geometry : bond 0.00298 ( 7925) covalent geometry : angle 0.53413 (10747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.904 Fit side-chains REVERT: A 123 MET cc_start: 0.5499 (mmp) cc_final: 0.5240 (mmm) REVERT: A 310 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 312 GLU cc_start: 0.8291 (tt0) cc_final: 0.7857 (tt0) REVERT: E 443 SER cc_start: 0.8563 (m) cc_final: 0.8152 (p) REVERT: L 19 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7929 (m) outliers start: 13 outliers final: 12 residues processed: 163 average time/residue: 0.2288 time to fit residues: 48.8142 Evaluate side-chains 169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 61 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 30 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 18 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110293 restraints weight = 13219.538| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.30 r_work: 0.3265 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 7936 Z= 0.117 Angle : 0.539 8.629 10768 Z= 0.280 Chirality : 0.041 0.137 1132 Planarity : 0.004 0.048 1385 Dihedral : 3.916 25.706 1099 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.57 % Allowed : 20.14 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.40 (0.28), residues: 935 helix: 1.41 (0.27), residues: 392 sheet: 1.25 (0.40), residues: 166 loop : 0.41 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.003 0.001 HIS A 374 PHE 0.010 0.001 PHE A 315 TYR 0.020 0.001 TYR A 243 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 3) link_NAG-ASN : angle 1.57778 ( 9) hydrogen bonds : bond 0.04555 ( 376) hydrogen bonds : angle 4.38982 ( 1028) metal coordination : bond 0.00092 ( 2) SS BOND : bond 0.00342 ( 6) SS BOND : angle 0.73102 ( 12) covalent geometry : bond 0.00272 ( 7925) covalent geometry : angle 0.53714 (10747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5961.34 seconds wall clock time: 105 minutes 19.44 seconds (6319.44 seconds total)