Starting phenix.real_space_refine on Fri Jul 19 11:23:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxw_38763/07_2024/8xxw_38763_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxw_38763/07_2024/8xxw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxw_38763/07_2024/8xxw_38763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxw_38763/07_2024/8xxw_38763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxw_38763/07_2024/8xxw_38763_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxw_38763/07_2024/8xxw_38763_neut.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 Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.75, per 1000 atoms: 0.87 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 - 3.50 Amino acid : False - 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: 2.53 Conformation dependent library (CDL) restraints added in 2.1 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: 0.87 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: 2.18 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 99.71 - 106.57: 219 106.57 - 113.42: 4103 113.42 - 120.27: 2938 120.27 - 127.13: 3383 127.13 - 133.98: 104 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 2.520 nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR A 279 " pdb=" OD1 ASN A 290 " model vdw 2.262 2.440 nonbonded pdb=" N GLU A 430 " pdb=" OE1 GLU A 430 " model vdw 2.296 2.520 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 116 " model vdw 2.303 2.440 ... (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 ========== 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: 10.940 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: 1.440 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- 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 7925 Z= 0.188 Angle : 0.567 6.790 10747 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.871 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: 0.2315 time to fit residues: 47.1326 Evaluate side-chains 153 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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: 0.7980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.0370 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7925 Z= 0.214 Angle : 0.523 8.717 10747 Z= 0.273 Chirality : 0.041 0.129 1132 Planarity : 0.005 0.063 1385 Dihedral : 4.366 39.998 1099 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.09 % Allowed : 18.82 % Favored : 80.10 % 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: 1.13 (0.28), residues: 935 helix: 1.25 (0.26), residues: 393 sheet: 0.96 (0.39), residues: 181 loop : 0.24 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE H 99 TYR 0.017 0.001 TYR A 243 ARG 0.004 0.000 ARG A 192 *********************** 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 169 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.5274 (mmp) cc_final: 0.4636 (mmm) REVERT: A 183 TYR cc_start: 0.7159 (t80) cc_final: 0.6902 (t80) REVERT: E 442 ASP cc_start: 0.8248 (m-30) cc_final: 0.8046 (m-30) REVERT: E 443 SER cc_start: 0.8588 (m) cc_final: 0.8140 (p) outliers start: 9 outliers final: 7 residues processed: 163 average time/residue: 0.2323 time to fit residues: 49.2286 Evaluate side-chains 165 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain E residue 471 GLU 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 47 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7925 Z= 0.274 Angle : 0.550 8.289 10747 Z= 0.288 Chirality : 0.042 0.134 1132 Planarity : 0.005 0.055 1385 Dihedral : 4.361 37.008 1099 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.81 % Allowed : 18.58 % 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: 1.03 (0.28), residues: 935 helix: 1.11 (0.26), residues: 398 sheet: 0.86 (0.39), residues: 183 loop : 0.26 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.004 0.001 HIS A 417 PHE 0.015 0.002 PHE H 99 TYR 0.016 0.002 TYR A 243 ARG 0.003 0.000 ARG A 192 *********************** 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 fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 0.843 Fit side-chains REVERT: A 123 MET cc_start: 0.5387 (mmp) cc_final: 0.4897 (mmm) REVERT: E 442 ASP cc_start: 0.8281 (m-30) cc_final: 0.8030 (m-30) REVERT: E 443 SER cc_start: 0.8604 (m) cc_final: 0.8149 (p) outliers start: 15 outliers final: 15 residues processed: 170 average time/residue: 0.2260 time to fit residues: 49.9142 Evaluate side-chains 176 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 75 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7925 Z= 0.210 Angle : 0.513 7.128 10747 Z= 0.267 Chirality : 0.041 0.128 1132 Planarity : 0.004 0.053 1385 Dihedral : 4.164 33.767 1099 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.93 % Allowed : 19.42 % 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: 1.20 (0.28), residues: 935 helix: 1.26 (0.27), residues: 398 sheet: 0.93 (0.39), residues: 182 loop : 0.35 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.004 0.001 HIS A 417 PHE 0.014 0.001 PHE H 99 TYR 0.018 0.001 TYR A 279 ARG 0.002 0.000 ARG A 306 *********************** 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 179 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.815 Fit side-chains REVERT: A 123 MET cc_start: 0.5207 (mmp) cc_final: 0.4838 (mmm) REVERT: E 443 SER cc_start: 0.8583 (m) cc_final: 0.8107 (p) REVERT: L 19 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7895 (m) outliers start: 16 outliers final: 13 residues processed: 170 average time/residue: 0.2361 time to fit residues: 51.9298 Evaluate side-chains 174 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET 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 10 SER Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7925 Z= 0.285 Angle : 0.552 7.269 10747 Z= 0.290 Chirality : 0.042 0.136 1132 Planarity : 0.004 0.053 1385 Dihedral : 4.297 32.988 1099 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.77 % Allowed : 18.46 % Favored : 78.77 % 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: 1.08 (0.28), residues: 935 helix: 1.20 (0.27), residues: 395 sheet: 0.86 (0.39), residues: 182 loop : 0.25 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.004 0.001 HIS A 417 PHE 0.015 0.002 PHE H 99 TYR 0.017 0.002 TYR A 279 ARG 0.002 0.000 ARG A 306 *********************** 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 189 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7784 (mm) cc_final: 0.7582 (mt) REVERT: A 123 MET cc_start: 0.5428 (mmp) cc_final: 0.5101 (mmm) REVERT: A 157 ASP cc_start: 0.6868 (p0) cc_final: 0.6547 (p0) REVERT: A 441 LYS cc_start: 0.7307 (ttmm) cc_final: 0.7043 (ttmm) REVERT: E 443 SER cc_start: 0.8574 (m) cc_final: 0.8156 (p) REVERT: L 19 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.7978 (m) outliers start: 23 outliers final: 20 residues processed: 179 average time/residue: 0.2256 time to fit residues: 52.7159 Evaluate side-chains 184 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 427 ASP 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 471 GLU 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 H residue 99 PHE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7925 Z= 0.227 Angle : 0.521 6.562 10747 Z= 0.273 Chirality : 0.041 0.130 1132 Planarity : 0.004 0.052 1385 Dihedral : 4.141 30.932 1099 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.14 % Allowed : 18.09 % Favored : 78.77 % 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: 1.19 (0.28), residues: 935 helix: 1.24 (0.26), residues: 400 sheet: 0.87 (0.39), residues: 182 loop : 0.40 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 417 PHE 0.014 0.001 PHE H 99 TYR 0.016 0.001 TYR A 279 ARG 0.002 0.000 ARG A 306 *********************** 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 187 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 0.932 Fit side-chains REVERT: A 88 ILE cc_start: 0.7776 (mm) cc_final: 0.7567 (mt) REVERT: A 123 MET cc_start: 0.5379 (mmp) cc_final: 0.5178 (mmm) REVERT: A 157 ASP cc_start: 0.6786 (p0) cc_final: 0.6537 (p0) REVERT: A 441 LYS cc_start: 0.7257 (ttmm) cc_final: 0.7005 (ttmm) REVERT: E 438 SER cc_start: 0.8207 (p) cc_final: 0.7814 (p) REVERT: L 4 MET cc_start: 0.8005 (mmm) cc_final: 0.7383 (mmm) REVERT: L 19 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7906 (m) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.2304 time to fit residues: 52.8649 Evaluate side-chains 181 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 432 ASN 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 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 58 VAL Chi-restraints excluded: chain L residue 70 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 66 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 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 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 7925 Z= 0.229 Angle : 0.532 6.286 10747 Z= 0.278 Chirality : 0.041 0.131 1132 Planarity : 0.004 0.052 1385 Dihedral : 4.106 29.521 1099 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.90 % Allowed : 18.82 % 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: 1.22 (0.28), residues: 935 helix: 1.30 (0.27), residues: 398 sheet: 0.85 (0.38), residues: 182 loop : 0.41 (0.34), residues: 355 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 0.014 0.001 PHE H 99 TYR 0.015 0.001 TYR A 243 ARG 0.005 0.000 ARG A 115 *********************** 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 179 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 0.805 Fit side-chains REVERT: A 88 ILE cc_start: 0.7784 (mm) cc_final: 0.7575 (mt) REVERT: A 123 MET cc_start: 0.5363 (mmp) cc_final: 0.5161 (mmm) REVERT: A 157 ASP cc_start: 0.6850 (p0) cc_final: 0.6595 (p0) REVERT: A 406 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7961 (mm-30) REVERT: A 441 LYS cc_start: 0.7286 (ttmm) cc_final: 0.7021 (ttmm) REVERT: E 438 SER cc_start: 0.8184 (p) cc_final: 0.7874 (p) REVERT: L 19 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7909 (m) outliers start: 24 outliers final: 22 residues processed: 171 average time/residue: 0.2351 time to fit residues: 52.8192 Evaluate side-chains 177 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 432 ASN 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 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 70 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 0.0370 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 7925 Z= 0.197 Angle : 0.511 5.817 10747 Z= 0.268 Chirality : 0.041 0.131 1132 Planarity : 0.004 0.051 1385 Dihedral : 3.995 27.698 1099 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.17 % Allowed : 19.66 % Favored : 78.17 % 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: 1.34 (0.28), residues: 935 helix: 1.37 (0.26), residues: 398 sheet: 1.11 (0.40), residues: 171 loop : 0.40 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.003 0.001 HIS A 540 PHE 0.012 0.001 PHE H 99 TYR 0.015 0.001 TYR A 243 ARG 0.003 0.000 ARG A 115 *********************** 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 176 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.630 Fit side-chains REVERT: A 157 ASP cc_start: 0.6875 (p0) cc_final: 0.6603 (p0) REVERT: A 441 LYS cc_start: 0.7240 (ttmm) cc_final: 0.6934 (ttmm) REVERT: E 438 SER cc_start: 0.8168 (p) cc_final: 0.7871 (p) REVERT: L 4 MET cc_start: 0.8004 (mmm) cc_final: 0.7459 (mmm) outliers start: 18 outliers final: 17 residues processed: 170 average time/residue: 0.3044 time to fit residues: 67.2398 Evaluate side-chains 173 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 103 ASN Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 432 ASN 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 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 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7925 Z= 0.290 Angle : 0.557 5.646 10747 Z= 0.294 Chirality : 0.043 0.142 1132 Planarity : 0.004 0.051 1385 Dihedral : 4.223 28.032 1099 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.41 % Allowed : 19.30 % 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: 1.11 (0.28), residues: 935 helix: 1.15 (0.26), residues: 398 sheet: 0.98 (0.39), residues: 176 loop : 0.30 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 477 HIS 0.003 0.001 HIS A 417 PHE 0.016 0.001 PHE H 99 TYR 0.015 0.002 TYR A 385 ARG 0.003 0.000 ARG A 115 *********************** 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 177 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 0.891 Fit side-chains REVERT: A 157 ASP cc_start: 0.6945 (p0) cc_final: 0.6697 (p0) REVERT: A 441 LYS cc_start: 0.7368 (ttmm) cc_final: 0.7038 (ttmm) REVERT: A 518 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7708 (mtp-110) REVERT: E 438 SER cc_start: 0.8215 (p) cc_final: 0.7871 (p) REVERT: L 4 MET cc_start: 0.7989 (mmm) cc_final: 0.7195 (mmm) outliers start: 20 outliers final: 19 residues processed: 169 average time/residue: 0.2284 time to fit residues: 50.3672 Evaluate side-chains 177 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 103 ASN 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 427 ASP Chi-restraints excluded: chain A residue 432 ASN 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 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 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.0270 chunk 59 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 7925 Z= 0.238 Angle : 0.538 6.581 10747 Z= 0.282 Chirality : 0.041 0.134 1132 Planarity : 0.004 0.052 1385 Dihedral : 4.110 27.785 1099 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.29 % Allowed : 19.66 % Favored : 78.05 % 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 (0.28), residues: 935 helix: 1.22 (0.26), residues: 398 sheet: 0.93 (0.38), residues: 180 loop : 0.32 (0.35), residues: 357 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 0.014 0.001 TYR A 279 ARG 0.003 0.000 ARG A 115 ********************** 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 180 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 157 ASP cc_start: 0.6944 (p0) cc_final: 0.6673 (p0) REVERT: A 310 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 312 GLU cc_start: 0.8370 (tt0) cc_final: 0.7926 (tt0) REVERT: A 441 LYS cc_start: 0.7310 (ttmm) cc_final: 0.7022 (ttmm) REVERT: E 438 SER cc_start: 0.8187 (p) cc_final: 0.7872 (p) REVERT: L 4 MET cc_start: 0.7959 (mmm) cc_final: 0.7508 (mmm) outliers start: 19 outliers final: 19 residues processed: 171 average time/residue: 0.2376 time to fit residues: 53.1365 Evaluate side-chains 184 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 103 ASN 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 427 ASP Chi-restraints excluded: chain A residue 432 ASN 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 471 GLU 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 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.0570 chunk 11 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 0.0050 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN E 394 ASN L 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110136 restraints weight = 18913.766| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.84 r_work: 0.3242 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.117 7925 Z= 0.158 Angle : 0.495 6.124 10747 Z= 0.259 Chirality : 0.040 0.125 1132 Planarity : 0.004 0.050 1385 Dihedral : 3.769 24.640 1099 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.17 % Allowed : 19.90 % Favored : 77.93 % 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: 1.49 (0.28), residues: 935 helix: 1.47 (0.26), residues: 398 sheet: 1.47 (0.40), residues: 163 loop : 0.37 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 594 HIS 0.004 0.001 HIS A 401 PHE 0.010 0.001 PHE A 315 TYR 0.014 0.001 TYR A 279 ARG 0.004 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.54 seconds wall clock time: 42 minutes 23.94 seconds (2543.94 seconds total)