Starting phenix.real_space_refine on Fri Jul 19 08:06:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbn_18316/07_2024/8qbn_18316_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbn_18316/07_2024/8qbn_18316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbn_18316/07_2024/8qbn_18316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbn_18316/07_2024/8qbn_18316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbn_18316/07_2024/8qbn_18316_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qbn_18316/07_2024/8qbn_18316_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 3 6.06 5 S 43 5.16 5 C 4399 2.51 5 N 1267 2.21 5 O 1309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7021 Number of models: 1 Model: "" Number of chains: 6 Chain: "7" Number of atoms: 3025 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 3043 Chain: "W" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3058 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 15, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "Y" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 935 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 473 SG CYS 7 300 38.682 73.606 62.497 1.00 51.16 S ATOM 605 SG CYS 7 322 37.760 74.057 66.052 1.00 55.21 S ATOM 3498 SG CYS W 300 26.251 64.816 41.836 1.00 44.85 S ATOM 3665 SG CYS W 322 26.214 64.719 38.134 1.00 49.11 S ATOM 6208 SG CYS Y 17 52.061 18.219 43.038 1.00 37.81 S ATOM 6227 SG CYS Y 20 50.220 20.004 40.221 1.00 39.91 S ATOM 6639 SG CYS Y 73 49.856 21.149 43.820 1.00 32.24 S ATOM 6662 SG CYS Y 76 48.366 17.906 42.809 1.00 36.22 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG 7 299 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG 7 299 " occ=0.50 residue: pdb=" N ATYR 7 330 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR 7 330 " occ=0.50 Time building chain proxies: 6.27, per 1000 atoms: 0.89 Number of scatterers: 7021 At special positions: 0 Unit cell: (78.12, 115.785, 110.205, 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 3 29.99 S 43 16.00 O 1309 8.00 N 1267 7.00 C 4399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 7 701 " pdb="ZN ZN 7 701 " - pdb=" ND1 HIS 7 303 " pdb="ZN ZN 7 701 " - pdb=" NE2 HIS 7 320 " pdb="ZN ZN 7 701 " - pdb=" SG CYS 7 322 " pdb="ZN ZN 7 701 " - pdb=" SG CYS 7 300 " pdb=" ZN W 701 " pdb="ZN ZN W 701 " - pdb=" ND1 HIS W 303 " pdb="ZN ZN W 701 " - pdb=" NE2 HIS W 320 " pdb="ZN ZN W 701 " - pdb=" SG CYS W 300 " pdb="ZN ZN W 701 " - pdb=" SG CYS W 322 " pdb=" ZN Y 501 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 17 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 20 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 73 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 76 " Number of angles added : 10 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 16 sheets defined 11.8% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain '7' and resid 121 through 139 removed outlier: 3.804A pdb=" N GLY 7 139 " --> pdb=" O LEU 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 142 through 152 Processing helix chain '7' and resid 283 through 299 removed outlier: 3.628A pdb=" N THR 7 287 " --> pdb=" O ARG 7 283 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N AARG 7 299 " --> pdb=" O LEU 7 295 " (cutoff:3.500A) Processing helix chain '7' and resid 323 through 327 Processing helix chain 'W' and resid 122 through 137 removed outlier: 3.723A pdb=" N GLY W 137 " --> pdb=" O GLN W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 151 Processing helix chain 'W' and resid 283 through 299 removed outlier: 3.735A pdb=" N THR W 287 " --> pdb=" O ARG W 283 " (cutoff:3.500A) Processing helix chain 'W' and resid 323 through 326 removed outlier: 4.028A pdb=" N GLN W 326 " --> pdb=" O SER W 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 323 through 326' Processing helix chain 'Y' and resid 89 through 94 removed outlier: 4.503A pdb=" N TYR Y 94 " --> pdb=" O SER Y 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '7' and resid 330 through 335 removed outlier: 6.543A pdb=" N ILE 7 624 " --> pdb=" O GLN 7 332 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE 7 334 " --> pdb=" O VAL 7 622 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL 7 622 " --> pdb=" O ILE 7 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '7' and resid 342 through 347 removed outlier: 3.638A pdb=" N PHE 7 344 " --> pdb=" O GLY 7 357 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL 7 363 " --> pdb=" O THR 7 380 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR 7 380 " --> pdb=" O VAL 7 363 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE 7 365 " --> pdb=" O LEU 7 378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '7' and resid 390 through 393 removed outlier: 4.034A pdb=" N TYR 7 390 " --> pdb=" O CYS 7 403 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '7' and resid 435 through 438 removed outlier: 3.530A pdb=" N SER 7 435 " --> pdb=" O GLY 7 448 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY 7 448 " --> pdb=" O SER 7 435 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP 7 458 " --> pdb=" O LEU 7 463 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU 7 463 " --> pdb=" O ASP 7 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '7' and resid 474 through 477 removed outlier: 3.696A pdb=" N CYS 7 474 " --> pdb=" O SER 7 487 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE 7 493 " --> pdb=" O ILE 7 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '7' and resid 513 through 518 removed outlier: 3.970A pdb=" N SER 7 515 " --> pdb=" O ASN 7 528 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL 7 534 " --> pdb=" O LYS 7 547 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS 7 547 " --> pdb=" O VAL 7 534 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU 7 536 " --> pdb=" O VAL 7 545 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '7' and resid 560 through 563 removed outlier: 3.649A pdb=" N ALA 7 591 " --> pdb=" O ILE 7 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 328 through 335 removed outlier: 5.021A pdb=" N THR W 331 " --> pdb=" O GLY W 626 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY W 626 " --> pdb=" O THR W 331 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN W 333 " --> pdb=" O ILE W 624 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS W 602 " --> pdb=" O ALA W 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 342 through 347 removed outlier: 3.566A pdb=" N SER W 358 " --> pdb=" O THR W 362 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR W 362 " --> pdb=" O SER W 358 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS W 379 " --> pdb=" O ILE W 365 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLN W 367 " --> pdb=" O LEU W 377 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU W 377 " --> pdb=" O GLN W 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 391 through 393 removed outlier: 3.597A pdb=" N THR W 423 " --> pdb=" O LEU W 413 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN W 415 " --> pdb=" O LEU W 421 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU W 421 " --> pdb=" O ASN W 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 435 through 438 removed outlier: 4.130A pdb=" N PHE W 454 " --> pdb=" O TRP W 467 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP W 458 " --> pdb=" O LEU W 463 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU W 463 " --> pdb=" O ASP W 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 472 through 477 removed outlier: 3.623A pdb=" N CYS W 474 " --> pdb=" O SER W 487 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 513 through 518 removed outlier: 3.799A pdb=" N SER W 515 " --> pdb=" O ASN W 528 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG W 546 " --> pdb=" O LEU W 536 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP W 538 " --> pdb=" O LEU W 544 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU W 544 " --> pdb=" O ASP W 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 560 through 563 Processing sheet with id=AB6, first strand: chain 'Y' and resid 23 through 26 removed outlier: 6.684A pdb=" N ILE Y 23 " --> pdb=" O CYS Y 17 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS Y 17 " --> pdb=" O ILE Y 23 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR Y 25 " --> pdb=" O PHE Y 15 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 30 through 36 removed outlier: 7.048A pdb=" N LEU Y 44 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR Y 33 " --> pdb=" O ALA Y 42 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA Y 42 " --> pdb=" O THR Y 33 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL Y 99 " --> pdb=" O PHE Y 45 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU Y 80 " --> pdb=" O GLU Y 102 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS Y 79 " --> pdb=" O CYS Y 73 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS Y 73 " --> pdb=" O LYS Y 79 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY Y 81 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET Y 67 " --> pdb=" O GLU Y 85 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA Y 87 " --> pdb=" O ARG Y 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ARG Y 65 " --> pdb=" O ALA Y 87 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP Y 70 " --> pdb=" O GLU Y 55 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLU Y 55 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER Y 72 " --> pdb=" O TYR Y 53 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR Y 53 " --> pdb=" O SER Y 72 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 615 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: 2.50 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2373 1.34 - 1.46: 1626 1.46 - 1.58: 3119 1.58 - 1.71: 0 1.71 - 1.83: 56 Bond restraints: 7174 Sorted by residual: bond pdb=" N VAL Y 116 " pdb=" CA VAL Y 116 " ideal model delta sigma weight residual 1.460 1.494 -0.035 7.50e-03 1.78e+04 2.14e+01 bond pdb=" N VAL 7 507 " pdb=" CA VAL 7 507 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.26e+00 bond pdb=" N VAL W 603 " pdb=" CA VAL W 603 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 8.95e+00 bond pdb=" N TRP W 476 " pdb=" CA TRP W 476 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.18e-02 7.18e+03 7.67e+00 bond pdb=" N ILE 7 506 " pdb=" CA ILE 7 506 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.31e+00 ... (remaining 7169 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.07: 193 107.07 - 113.83: 4060 113.83 - 120.59: 2624 120.59 - 127.35: 2774 127.35 - 134.10: 104 Bond angle restraints: 9755 Sorted by residual: angle pdb=" N ARG W 324 " pdb=" CA ARG W 324 " pdb=" C ARG W 324 " ideal model delta sigma weight residual 113.15 108.54 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" CA ARG 7 504 " pdb=" C ARG 7 504 " pdb=" O ARG 7 504 " ideal model delta sigma weight residual 121.51 117.41 4.10 1.12e+00 7.97e-01 1.34e+01 angle pdb=" CA ILE W 518 " pdb=" C ILE W 518 " pdb=" O ILE W 518 " ideal model delta sigma weight residual 121.93 118.02 3.91 1.12e+00 7.97e-01 1.22e+01 angle pdb=" C SER 7 121 " pdb=" CA SER 7 121 " pdb=" CB SER 7 121 " ideal model delta sigma weight residual 111.78 104.12 7.66 2.20e+00 2.07e-01 1.21e+01 angle pdb=" CA HIS Y 115 " pdb=" CB HIS Y 115 " pdb=" CG HIS Y 115 " ideal model delta sigma weight residual 113.80 117.18 -3.38 1.00e+00 1.00e+00 1.14e+01 ... (remaining 9750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 3743 16.74 - 33.49: 373 33.49 - 50.23: 91 50.23 - 66.97: 16 66.97 - 83.72: 5 Dihedral angle restraints: 4228 sinusoidal: 1642 harmonic: 2586 Sorted by residual: dihedral pdb=" CA TYR W 302 " pdb=" C TYR W 302 " pdb=" N HIS W 303 " pdb=" CA HIS W 303 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" C SER 7 121 " pdb=" N SER 7 121 " pdb=" CA SER 7 121 " pdb=" CB SER 7 121 " ideal model delta harmonic sigma weight residual -122.60 -113.78 -8.82 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA CYS W 561 " pdb=" C CYS W 561 " pdb=" N PHE W 562 " pdb=" CA PHE W 562 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 808 0.049 - 0.097: 206 0.097 - 0.146: 69 0.146 - 0.194: 2 0.194 - 0.243: 4 Chirality restraints: 1089 Sorted by residual: chirality pdb=" CA SER 7 121 " pdb=" N SER 7 121 " pdb=" C SER 7 121 " pdb=" CB SER 7 121 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA VAL W 603 " pdb=" N VAL W 603 " pdb=" C VAL W 603 " pdb=" CB VAL W 603 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE 7 506 " pdb=" N ILE 7 506 " pdb=" C ILE 7 506 " pdb=" CB ILE 7 506 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1086 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP W 605 " 0.014 2.00e-02 2.50e+03 1.47e-02 5.38e+00 pdb=" CG TRP W 605 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP W 605 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP W 605 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP W 605 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP W 605 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP W 605 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 605 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 605 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP W 605 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN W 439 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO W 440 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO W 440 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO W 440 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG 7 504 " 0.148 9.50e-02 1.11e+02 6.63e-02 2.80e+00 pdb=" NE ARG 7 504 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG 7 504 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG 7 504 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 7 504 " 0.003 2.00e-02 2.50e+03 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 593 2.74 - 3.28: 6068 3.28 - 3.82: 10575 3.82 - 4.36: 13006 4.36 - 4.90: 23811 Nonbonded interactions: 54053 Sorted by model distance: nonbonded pdb=" OG SER W 574 " pdb=" OD1 ASP W 576 " model vdw 2.206 2.440 nonbonded pdb=" O GLU W 341 " pdb=" OG SER W 358 " model vdw 2.223 2.440 nonbonded pdb=" OG SER 7 574 " pdb=" OD1 ASP 7 576 " model vdw 2.261 2.440 nonbonded pdb=" O ASN 7 304 " pdb=" OD1 ASN 7 304 " model vdw 2.291 3.040 nonbonded pdb=" OG SER W 428 " pdb=" OD1 ASP W 431 " model vdw 2.307 2.440 ... (remaining 54048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '7' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 123 or (resid 124 through 125 and (name N or name CA or \ name C or name O or name CB )) or resid 126 through 141 or (resid 142 and (name \ N or name CA or name C or name O or name CB )) or resid 143 through 298 or resi \ d 300 through 312 or (resid 313 and (name N or name CA or name C or name O or na \ me CB )) or resid 314 through 320 or (resid 321 and (name N or name CA or name C \ or name O or name CB )) or resid 322 through 329 or resid 331 through 375 or (r \ esid 376 and (name N or name CA or name C or name O or name CB )) or resid 377 t \ hrough 419 or (resid 420 and (name N or name CA or name C or name O or name CB ) \ ) or resid 421 through 481 or (resid 482 and (name N or name CA or name C or nam \ e O or name CB )) or resid 483 through 498 or (resid 499 and (name N or name CA \ or name C or name O or name CB )) or resid 500 through 629 or resid 701)) selection = (chain 'W' and (resid 121 through 124 or (resid 125 and (name N or name CA or na \ me C or name O or name CB )) or resid 126 through 140 or (resid 141 through 142 \ and (name N or name CA or name C or name O or name CB )) or resid 143 through 14 \ 4 or (resid 145 and (name N or name CA or name C or name O or name CB )) or resi \ d 146 through 154 or (resid 155 and (name N or name CA or name C or name O or na \ me CB )) or resid 276 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 293 or (resid 294 and (name N or n \ ame CA or name C or name O or name CB )) or resid 295 through 298 or resid 300 t \ hrough 304 or (resid 305 through 308 and (name N or name CA or name C or name O \ or name CB )) or resid 313 through 322 or (resid 323 and (name N or name CA or n \ ame C or name O or name CB )) or resid 324 through 329 or resid 331 through 405 \ or (resid 406 through 407 and (name N or name CA or name C or name O or name CB \ )) or resid 408 through 457 or (resid 458 and (name N or name CA or name C or na \ me O or name CB )) or resid 459 or (resid 460 and (name N or name CA or name C o \ r name O or name CB )) or resid 461 through 554 or (resid 555 through 556 and (n \ ame N or name CA or name C or name O or name CB )) or resid 557 through 629 or r \ esid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.280 Find NCS groups from input model: 0.380 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7174 Z= 0.244 Angle : 0.589 7.655 9755 Z= 0.344 Chirality : 0.048 0.243 1089 Planarity : 0.004 0.066 1263 Dihedral : 14.296 83.717 2560 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.27 % Allowed : 0.53 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.28), residues: 891 helix: 2.75 (0.59), residues: 87 sheet: -0.12 (0.31), residues: 274 loop : -1.18 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP W 605 HIS 0.008 0.001 HIS W 565 PHE 0.020 0.002 PHE 7 454 TYR 0.009 0.001 TYR W 330 ARG 0.006 0.000 ARG 7 504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.852 Fit side-chains REVERT: 7 318 ILE cc_start: 0.8770 (mt) cc_final: 0.8241 (tp) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2117 time to fit residues: 14.9235 Evaluate side-chains 37 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 41 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 417 GLN Y 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7174 Z= 0.147 Angle : 0.486 7.653 9755 Z= 0.258 Chirality : 0.044 0.233 1089 Planarity : 0.003 0.046 1263 Dihedral : 4.174 16.611 974 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.53 % Allowed : 3.99 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.28), residues: 891 helix: 3.09 (0.57), residues: 90 sheet: 0.16 (0.31), residues: 277 loop : -1.06 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 7 605 HIS 0.003 0.001 HIS W 303 PHE 0.015 0.001 PHE 7 454 TYR 0.009 0.001 TYR 7 302 ARG 0.004 0.000 ARG W 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.862 Fit side-chains REVERT: 7 148 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7497 (mmm) REVERT: 7 318 ILE cc_start: 0.8592 (mt) cc_final: 0.8004 (tp) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.1638 time to fit residues: 11.4455 Evaluate side-chains 44 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain Y residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 384 HIS W 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7174 Z= 0.259 Angle : 0.538 6.028 9755 Z= 0.285 Chirality : 0.045 0.175 1089 Planarity : 0.004 0.040 1263 Dihedral : 4.388 16.813 974 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.06 % Allowed : 6.78 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.28), residues: 891 helix: 2.57 (0.57), residues: 97 sheet: 0.20 (0.32), residues: 270 loop : -1.12 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 7 605 HIS 0.006 0.001 HIS W 577 PHE 0.028 0.002 PHE 7 454 TYR 0.010 0.001 TYR W 390 ARG 0.004 0.000 ARG 7 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.858 Fit side-chains REVERT: 7 148 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7638 (mmm) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.1784 time to fit residues: 11.3546 Evaluate side-chains 45 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 318 ILE Chi-restraints excluded: chain W residue 590 ILE Chi-restraints excluded: chain Y residue 23 ILE Chi-restraints excluded: chain Y residue 100 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7174 Z= 0.179 Angle : 0.481 5.987 9755 Z= 0.257 Chirality : 0.044 0.153 1089 Planarity : 0.003 0.037 1263 Dihedral : 4.219 16.181 974 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.93 % Allowed : 8.78 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.28), residues: 891 helix: 2.66 (0.57), residues: 97 sheet: 0.18 (0.31), residues: 270 loop : -1.07 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 7 605 HIS 0.004 0.001 HIS W 577 PHE 0.017 0.002 PHE 7 454 TYR 0.009 0.001 TYR 7 302 ARG 0.002 0.000 ARG Y 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.897 Fit side-chains REVERT: 7 148 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: Y 14 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8507 (mt) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.1743 time to fit residues: 11.0879 Evaluate side-chains 45 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain W residue 318 ILE Chi-restraints excluded: chain W residue 590 ILE Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 23 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 28 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: W 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7174 Z= 0.249 Angle : 0.521 6.390 9755 Z= 0.277 Chirality : 0.045 0.163 1089 Planarity : 0.003 0.040 1263 Dihedral : 4.345 16.610 974 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.06 % Allowed : 10.11 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.28), residues: 891 helix: 2.59 (0.57), residues: 98 sheet: 0.15 (0.31), residues: 272 loop : -1.13 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 7 605 HIS 0.007 0.001 HIS W 577 PHE 0.026 0.002 PHE 7 454 TYR 0.011 0.001 TYR W 390 ARG 0.003 0.000 ARG Y 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.778 Fit side-chains REVERT: 7 148 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7592 (mmm) REVERT: Y 14 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8579 (mt) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.1591 time to fit residues: 10.2210 Evaluate side-chains 45 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain W residue 318 ILE Chi-restraints excluded: chain W residue 590 ILE Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 23 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.0670 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 528 ASN W 417 GLN ** W 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7174 Z= 0.341 Angle : 0.578 7.487 9755 Z= 0.306 Chirality : 0.047 0.174 1089 Planarity : 0.004 0.043 1263 Dihedral : 4.633 18.022 974 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.46 % Allowed : 10.90 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 891 helix: 2.48 (0.57), residues: 97 sheet: 0.05 (0.31), residues: 276 loop : -1.18 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 7 605 HIS 0.009 0.001 HIS W 577 PHE 0.033 0.002 PHE 7 454 TYR 0.014 0.002 TYR W 390 ARG 0.004 0.000 ARG Y 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.790 Fit side-chains REVERT: 7 148 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7623 (mmm) REVERT: Y 14 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8557 (mt) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.1732 time to fit residues: 11.9159 Evaluate side-chains 47 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 318 ILE Chi-restraints excluded: chain W residue 502 THR Chi-restraints excluded: chain W residue 590 ILE Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 23 ILE Chi-restraints excluded: chain Y residue 100 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 39 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 528 ASN W 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7174 Z= 0.216 Angle : 0.508 7.713 9755 Z= 0.271 Chirality : 0.044 0.160 1089 Planarity : 0.003 0.041 1263 Dihedral : 4.431 16.619 974 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.46 % Allowed : 11.70 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.28), residues: 891 helix: 2.52 (0.57), residues: 97 sheet: 0.11 (0.31), residues: 274 loop : -1.15 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 582 HIS 0.005 0.001 HIS W 577 PHE 0.020 0.002 PHE 7 454 TYR 0.010 0.001 TYR W 390 ARG 0.002 0.000 ARG Y 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.865 Fit side-chains REVERT: 7 148 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7636 (mmm) REVERT: Y 14 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8551 (mt) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.1643 time to fit residues: 11.2113 Evaluate side-chains 47 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain W residue 318 ILE Chi-restraints excluded: chain W residue 502 THR Chi-restraints excluded: chain W residue 517 THR Chi-restraints excluded: chain W residue 552 THR Chi-restraints excluded: chain W residue 590 ILE Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 23 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7174 Z= 0.240 Angle : 0.519 8.234 9755 Z= 0.276 Chirality : 0.045 0.162 1089 Planarity : 0.003 0.041 1263 Dihedral : 4.436 16.548 974 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.60 % Allowed : 11.57 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.28), residues: 891 helix: 2.47 (0.57), residues: 98 sheet: 0.11 (0.31), residues: 275 loop : -1.15 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 7 582 HIS 0.006 0.001 HIS W 577 PHE 0.023 0.002 PHE 7 454 TYR 0.011 0.001 TYR W 390 ARG 0.003 0.000 ARG Y 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 0.883 Fit side-chains REVERT: 7 148 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7654 (mmm) REVERT: Y 14 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8551 (mt) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.1742 time to fit residues: 11.7569 Evaluate side-chains 46 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain W residue 318 ILE Chi-restraints excluded: chain W residue 502 THR Chi-restraints excluded: chain W residue 517 THR Chi-restraints excluded: chain W residue 552 THR Chi-restraints excluded: chain W residue 590 ILE Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 23 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.5980 chunk 81 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 chunk 51 optimal weight: 0.0070 chunk 83 optimal weight: 2.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 417 GLN ** W 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7174 Z= 0.156 Angle : 0.468 8.075 9755 Z= 0.249 Chirality : 0.043 0.146 1089 Planarity : 0.003 0.039 1263 Dihedral : 4.176 15.765 974 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.33 % Allowed : 11.97 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.28), residues: 891 helix: 2.60 (0.57), residues: 98 sheet: 0.19 (0.31), residues: 279 loop : -1.03 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 7 582 HIS 0.003 0.001 HIS W 577 PHE 0.015 0.001 PHE 7 454 TYR 0.008 0.001 TYR 7 302 ARG 0.002 0.000 ARG W 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.849 Fit side-chains REVERT: 7 148 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7536 (mmm) REVERT: Y 14 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8499 (mt) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.1607 time to fit residues: 11.2734 Evaluate side-chains 46 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 600 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 502 THR Chi-restraints excluded: chain W residue 517 THR Chi-restraints excluded: chain W residue 552 THR Chi-restraints excluded: chain W residue 590 ILE Chi-restraints excluded: chain Y residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 55 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7174 Z= 0.189 Angle : 0.484 8.296 9755 Z= 0.257 Chirality : 0.044 0.152 1089 Planarity : 0.003 0.040 1263 Dihedral : 4.213 15.609 974 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.20 % Allowed : 12.10 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.28), residues: 891 helix: 2.62 (0.57), residues: 98 sheet: 0.16 (0.31), residues: 284 loop : -0.99 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 7 582 HIS 0.004 0.001 HIS W 577 PHE 0.019 0.002 PHE 7 454 TYR 0.008 0.001 TYR W 390 ARG 0.002 0.000 ARG Y 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.860 Fit side-chains REVERT: 7 148 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7564 (mmm) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 0.1629 time to fit residues: 10.9740 Evaluate side-chains 45 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 600 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain W residue 502 THR Chi-restraints excluded: chain W residue 517 THR Chi-restraints excluded: chain W residue 552 THR Chi-restraints excluded: chain W residue 590 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.090031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.074331 restraints weight = 38344.730| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.07 r_work: 0.2691 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7174 Z= 0.240 Angle : 0.514 8.234 9755 Z= 0.272 Chirality : 0.045 0.163 1089 Planarity : 0.003 0.041 1263 Dihedral : 4.329 16.039 974 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.86 % Allowed : 11.44 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.28), residues: 891 helix: 2.55 (0.57), residues: 98 sheet: 0.19 (0.31), residues: 273 loop : -1.09 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 7 582 HIS 0.006 0.001 HIS W 577 PHE 0.022 0.002 PHE 7 454 TYR 0.010 0.001 TYR W 390 ARG 0.002 0.000 ARG Y 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.37 seconds wall clock time: 31 minutes 7.65 seconds (1867.65 seconds total)