Starting phenix.real_space_refine on Tue Feb 13 21:01:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2024/7y9v_33693_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2024/7y9v_33693.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/7y9v_33693/02_2024/7y9v_33693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2024/7y9v_33693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2024/7y9v_33693_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2024/7y9v_33693_neut_updated.pdb" } 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= 0.003 sd= 0.087 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5062 2.51 5 N 1272 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7734 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2957 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "B" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2957 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.20, per 1000 atoms: 0.54 Number of scatterers: 7734 At special positions: 0 Unit cell: (111.28, 119.6, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1344 8.00 N 1272 7.00 C 5062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 100 " distance=2.03 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 12 sheets defined 46.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 3.645A pdb=" N VAL A 10 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Proline residue: A 16 - end of helix removed outlier: 3.620A pdb=" N ALA A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.722A pdb=" N ASN A 43 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.605A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.692A pdb=" N THR A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 129 through 142 removed outlier: 4.109A pdb=" N VAL A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.517A pdb=" N LEU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.988A pdb=" N ARG A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.600A pdb=" N SER A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 508 through 511 No H-bonds generated for 'chain 'A' and resid 508 through 511' Processing helix chain 'A' and resid 514 through 528 removed outlier: 3.776A pdb=" N MET A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 546 removed outlier: 4.021A pdb=" N PHE A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 567 through 577 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 597 through 607 removed outlier: 4.052A pdb=" N VAL A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 619 removed outlier: 3.695A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 29 removed outlier: 3.645A pdb=" N VAL B 10 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Proline residue: B 16 - end of helix removed outlier: 3.620A pdb=" N ALA B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.722A pdb=" N ASN B 43 " --> pdb=" O CYS B 39 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.604A pdb=" N ALA B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.691A pdb=" N THR B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 129 through 142 removed outlier: 4.109A pdb=" N VAL B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 removed outlier: 3.518A pdb=" N LEU B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 458 through 473 removed outlier: 3.988A pdb=" N ARG B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 removed outlier: 3.601A pdb=" N SER B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 506 No H-bonds generated for 'chain 'B' and resid 503 through 506' Processing helix chain 'B' and resid 508 through 511 No H-bonds generated for 'chain 'B' and resid 508 through 511' Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.776A pdb=" N MET B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 546 removed outlier: 4.020A pdb=" N PHE B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 567 through 577 Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'B' and resid 597 through 607 removed outlier: 4.052A pdb=" N VAL B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 removed outlier: 3.695A pdb=" N LEU B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 192 through 196 removed outlier: 7.244A pdb=" N VAL A 204 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 175 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 206 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A 177 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.920A pdb=" N SER C 29 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 11 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 25 " --> pdb=" O SER C 11 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 15 through 17 removed outlier: 6.162A pdb=" N THR C 116 " --> pdb=" O VAL C 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.524A pdb=" N ASP C 77 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 101 through 103 Processing sheet with id= F, first strand: chain 'C' and resid 39 through 42 removed outlier: 3.754A pdb=" N TRP C 40 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 53 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG C 42 " --> pdb=" O TRP C 51 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TRP C 51 " --> pdb=" O ARG C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 7 through 11 removed outlier: 3.921A pdb=" N SER D 29 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 11 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 25 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.163A pdb=" N THR D 116 " --> pdb=" O VAL D 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.524A pdb=" N ASP D 77 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 101 through 103 Processing sheet with id= K, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.755A pdb=" N TRP D 40 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 53 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG D 42 " --> pdb=" O TRP D 51 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TRP D 51 " --> pdb=" O ARG D 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 192 through 196 removed outlier: 7.244A pdb=" N VAL B 204 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B 175 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 206 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL B 177 " --> pdb=" O VAL B 206 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 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: 1.14 - 1.27: 1180 1.27 - 1.41: 2058 1.41 - 1.54: 4482 1.54 - 1.67: 96 1.67 - 1.80: 100 Bond restraints: 7916 Sorted by residual: bond pdb=" CA LEU B 147 " pdb=" C LEU B 147 " ideal model delta sigma weight residual 1.519 1.361 0.158 1.01e-02 9.80e+03 2.46e+02 bond pdb=" CA LEU A 147 " pdb=" C LEU A 147 " ideal model delta sigma weight residual 1.519 1.361 0.158 1.01e-02 9.80e+03 2.46e+02 bond pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 1.526 1.405 0.121 1.11e-02 8.12e+03 1.19e+02 bond pdb=" CA ASN A 112 " pdb=" C ASN A 112 " ideal model delta sigma weight residual 1.526 1.406 0.121 1.11e-02 8.12e+03 1.18e+02 bond pdb=" CA ALA B 561 " pdb=" C ALA B 561 " ideal model delta sigma weight residual 1.522 1.421 0.101 1.39e-02 5.18e+03 5.31e+01 ... (remaining 7911 not shown) Histogram of bond angle deviations from ideal: 95.72 - 103.39: 124 103.39 - 111.06: 2985 111.06 - 118.74: 3212 118.74 - 126.41: 4273 126.41 - 134.08: 168 Bond angle restraints: 10762 Sorted by residual: angle pdb=" N SER A 479 " pdb=" CA SER A 479 " pdb=" C SER A 479 " ideal model delta sigma weight residual 114.04 98.18 15.86 1.24e+00 6.50e-01 1.64e+02 angle pdb=" N SER B 479 " pdb=" CA SER B 479 " pdb=" C SER B 479 " ideal model delta sigma weight residual 114.04 98.19 15.85 1.24e+00 6.50e-01 1.63e+02 angle pdb=" N LEU A 147 " pdb=" CA LEU A 147 " pdb=" C LEU A 147 " ideal model delta sigma weight residual 112.72 98.40 14.32 1.28e+00 6.10e-01 1.25e+02 angle pdb=" N LEU B 147 " pdb=" CA LEU B 147 " pdb=" C LEU B 147 " ideal model delta sigma weight residual 112.72 98.45 14.27 1.28e+00 6.10e-01 1.24e+02 angle pdb=" C ASN A 112 " pdb=" CA ASN A 112 " pdb=" CB ASN A 112 " ideal model delta sigma weight residual 112.05 102.06 9.99 1.52e+00 4.33e-01 4.32e+01 ... (remaining 10757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 4408 16.93 - 33.85: 198 33.85 - 50.78: 44 50.78 - 67.71: 2 67.71 - 84.63: 4 Dihedral angle restraints: 4656 sinusoidal: 1794 harmonic: 2862 Sorted by residual: dihedral pdb=" CA GLN C 56 " pdb=" C GLN C 56 " pdb=" N SER C 57 " pdb=" CA SER C 57 " ideal model delta harmonic sigma weight residual -180.00 -138.53 -41.47 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA GLN D 56 " pdb=" C GLN D 56 " pdb=" N SER D 57 " pdb=" CA SER D 57 " ideal model delta harmonic sigma weight residual -180.00 -138.55 -41.45 0 5.00e+00 4.00e-02 6.87e+01 dihedral pdb=" C LEU A 147 " pdb=" N LEU A 147 " pdb=" CA LEU A 147 " pdb=" CB LEU A 147 " ideal model delta harmonic sigma weight residual -122.60 -107.71 -14.89 0 2.50e+00 1.60e-01 3.55e+01 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 939 0.065 - 0.130: 253 0.130 - 0.196: 44 0.196 - 0.261: 7 0.261 - 0.326: 3 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CB ILE C 55 " pdb=" CA ILE C 55 " pdb=" CG1 ILE C 55 " pdb=" CG2 ILE C 55 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE D 55 " pdb=" CA ILE D 55 " pdb=" CG1 ILE D 55 " pdb=" CG2 ILE D 55 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE D 35 " pdb=" CA ILE D 35 " pdb=" CG1 ILE D 35 " pdb=" CG2 ILE D 35 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1243 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 551 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO A 552 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 551 " -0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO B 552 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 552 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 552 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 140 " -0.013 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C GLN A 140 " 0.043 2.00e-02 2.50e+03 pdb=" O GLN A 140 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS A 141 " -0.015 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 73 2.63 - 3.19: 6478 3.19 - 3.76: 11353 3.76 - 4.33: 16630 4.33 - 4.90: 26885 Nonbonded interactions: 61419 Sorted by model distance: nonbonded pdb=" NH2 ARG D 71 " pdb=" O SER D 89 " model vdw 2.057 2.520 nonbonded pdb=" NH2 ARG C 71 " pdb=" O SER C 89 " model vdw 2.057 2.520 nonbonded pdb=" NE1 TRP D 37 " pdb=" OE2 GLU D 39 " model vdw 2.227 2.520 nonbonded pdb=" NE1 TRP C 37 " pdb=" OE2 GLU C 39 " model vdw 2.228 2.520 nonbonded pdb=" O THR B 458 " pdb=" OG1 THR B 462 " model vdw 2.320 2.440 ... (remaining 61414 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=1.00 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: 1.250 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: 0.010 Extract box with map and model: 3.880 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.120 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.013 0.158 7916 Z= 0.862 Angle : 1.209 15.856 10762 Z= 0.690 Chirality : 0.063 0.326 1246 Planarity : 0.009 0.066 1322 Dihedral : 10.859 84.631 2810 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.48 % Allowed : 3.13 % Favored : 96.39 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -5.91 (0.18), residues: 976 helix: -4.55 (0.09), residues: 540 sheet: -2.50 (0.46), residues: 116 loop : -2.74 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 31 HIS 0.006 0.002 HIS B 594 PHE 0.021 0.003 PHE B 58 TYR 0.034 0.003 TYR A 617 ARG 0.013 0.001 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 0.873 Fit side-chains REVERT: A 32 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8376 (mmtt) REVERT: A 122 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8307 (mtpp) REVERT: A 147 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 181 ILE cc_start: 0.8457 (mt) cc_final: 0.8224 (mt) REVERT: A 201 LYS cc_start: 0.7289 (mttt) cc_final: 0.6916 (mmtt) REVERT: A 459 SER cc_start: 0.8610 (t) cc_final: 0.8205 (p) REVERT: A 505 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8356 (mmmt) REVERT: A 512 ASP cc_start: 0.8374 (m-30) cc_final: 0.7925 (m-30) REVERT: C 55 ILE cc_start: 0.7367 (tp) cc_final: 0.7102 (tt) REVERT: B 9 HIS cc_start: 0.8203 (m-70) cc_final: 0.7902 (m170) REVERT: B 29 LYS cc_start: 0.7516 (tppt) cc_final: 0.7224 (tppt) REVERT: B 32 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8204 (mmtm) REVERT: B 122 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8303 (mtpp) REVERT: B 181 ILE cc_start: 0.8458 (mt) cc_final: 0.8236 (mt) REVERT: B 201 LYS cc_start: 0.7210 (mttt) cc_final: 0.6783 (mmtt) REVERT: B 459 SER cc_start: 0.8487 (t) cc_final: 0.8204 (p) REVERT: B 467 ILE cc_start: 0.8984 (mm) cc_final: 0.8641 (mt) REVERT: B 505 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8313 (mmmt) REVERT: B 512 ASP cc_start: 0.8358 (m-30) cc_final: 0.7759 (m-30) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.2743 time to fit residues: 65.3853 Evaluate side-chains 129 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 164 GLN B 43 ASN B 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7916 Z= 0.205 Angle : 0.601 6.813 10762 Z= 0.315 Chirality : 0.043 0.144 1246 Planarity : 0.006 0.048 1322 Dihedral : 6.743 83.589 1074 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.45 % Allowed : 9.40 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.78 (0.23), residues: 976 helix: -2.61 (0.17), residues: 536 sheet: -2.15 (0.46), residues: 120 loop : -1.98 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 144 HIS 0.001 0.001 HIS B 570 PHE 0.014 0.002 PHE A 525 TYR 0.012 0.001 TYR C 41 ARG 0.006 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.906 Fit side-chains REVERT: A 1 MET cc_start: 0.5482 (ppp) cc_final: 0.5229 (ppp) REVERT: A 21 MET cc_start: 0.8643 (ttp) cc_final: 0.8311 (ttt) REVERT: A 32 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8362 (mmtt) REVERT: A 201 LYS cc_start: 0.7122 (mttt) cc_final: 0.6618 (mmtt) REVERT: A 459 SER cc_start: 0.8410 (t) cc_final: 0.8160 (p) REVERT: A 502 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 505 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8309 (mmmt) REVERT: A 512 ASP cc_start: 0.8306 (m-30) cc_final: 0.7821 (m-30) REVERT: A 517 MET cc_start: 0.8328 (mmm) cc_final: 0.8063 (mmm) REVERT: B 1 MET cc_start: 0.5449 (ppp) cc_final: 0.5087 (ppp) REVERT: B 21 MET cc_start: 0.8547 (ttp) cc_final: 0.8285 (ttt) REVERT: B 29 LYS cc_start: 0.7676 (tppt) cc_final: 0.7404 (tppt) REVERT: B 32 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8231 (mmtt) REVERT: B 173 VAL cc_start: 0.9039 (t) cc_final: 0.8686 (m) REVERT: B 201 LYS cc_start: 0.7078 (mttt) cc_final: 0.6632 (mmtt) REVERT: B 505 LYS cc_start: 0.8559 (mmtp) cc_final: 0.8297 (mmmt) REVERT: B 512 ASP cc_start: 0.8260 (m-30) cc_final: 0.7967 (m-30) REVERT: B 517 MET cc_start: 0.8274 (mmm) cc_final: 0.7906 (mmm) outliers start: 12 outliers final: 7 residues processed: 160 average time/residue: 0.2084 time to fit residues: 44.2781 Evaluate side-chains 136 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7916 Z= 0.215 Angle : 0.542 5.571 10762 Z= 0.283 Chirality : 0.042 0.140 1246 Planarity : 0.005 0.044 1322 Dihedral : 6.135 79.054 1072 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.65 % Allowed : 11.69 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.50 (0.25), residues: 976 helix: -1.41 (0.21), residues: 532 sheet: -1.91 (0.44), residues: 138 loop : -1.55 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 144 HIS 0.006 0.001 HIS A 57 PHE 0.009 0.002 PHE D 72 TYR 0.011 0.001 TYR C 41 ARG 0.004 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 0.856 Fit side-chains REVERT: A 21 MET cc_start: 0.8575 (ttp) cc_final: 0.8299 (ttt) REVERT: A 32 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8304 (mmtt) REVERT: A 180 ASP cc_start: 0.8072 (t0) cc_final: 0.7854 (t0) REVERT: A 201 LYS cc_start: 0.7228 (mttt) cc_final: 0.6755 (mmtt) REVERT: A 459 SER cc_start: 0.8498 (t) cc_final: 0.8235 (p) REVERT: A 505 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8309 (mmmt) REVERT: A 512 ASP cc_start: 0.8275 (m-30) cc_final: 0.7843 (m-30) REVERT: A 517 MET cc_start: 0.8376 (mmm) cc_final: 0.8016 (mmm) REVERT: C 56 GLN cc_start: 0.6360 (pt0) cc_final: 0.6120 (pt0) REVERT: B 1 MET cc_start: 0.5379 (ppp) cc_final: 0.5106 (ppp) REVERT: B 21 MET cc_start: 0.8536 (ttp) cc_final: 0.8257 (ttt) REVERT: B 29 LYS cc_start: 0.7689 (tppt) cc_final: 0.7451 (tppt) REVERT: B 32 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8186 (mmtt) REVERT: B 173 VAL cc_start: 0.9102 (t) cc_final: 0.8742 (m) REVERT: B 201 LYS cc_start: 0.7101 (mttt) cc_final: 0.6660 (mmtt) REVERT: B 505 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8285 (mmmt) REVERT: B 512 ASP cc_start: 0.8267 (m-30) cc_final: 0.8005 (m-30) REVERT: B 517 MET cc_start: 0.8339 (mmm) cc_final: 0.7975 (mmm) outliers start: 22 outliers final: 12 residues processed: 159 average time/residue: 0.2099 time to fit residues: 44.1255 Evaluate side-chains 149 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7916 Z= 0.315 Angle : 0.587 8.860 10762 Z= 0.302 Chirality : 0.045 0.160 1246 Planarity : 0.005 0.044 1322 Dihedral : 6.177 81.835 1072 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.34 % Allowed : 10.00 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.01 (0.26), residues: 976 helix: -0.98 (0.21), residues: 538 sheet: -1.63 (0.46), residues: 138 loop : -1.45 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.005 0.001 HIS A 57 PHE 0.010 0.002 PHE A 493 TYR 0.016 0.001 TYR B 617 ARG 0.004 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 0.913 Fit side-chains REVERT: A 21 MET cc_start: 0.8645 (ttp) cc_final: 0.8371 (ttt) REVERT: A 32 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8241 (mmtt) REVERT: A 201 LYS cc_start: 0.7328 (mttt) cc_final: 0.6880 (mmtt) REVERT: A 459 SER cc_start: 0.8535 (t) cc_final: 0.8209 (p) REVERT: A 467 ILE cc_start: 0.8841 (mm) cc_final: 0.8459 (mt) REVERT: A 505 LYS cc_start: 0.8577 (mmtp) cc_final: 0.8286 (mmmt) REVERT: A 512 ASP cc_start: 0.8277 (m-30) cc_final: 0.7847 (m-30) REVERT: A 517 MET cc_start: 0.8382 (mmm) cc_final: 0.7992 (mmm) REVERT: A 522 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8833 (tp) REVERT: C 56 GLN cc_start: 0.6484 (pt0) cc_final: 0.6284 (pt0) REVERT: D 56 GLN cc_start: 0.6779 (pt0) cc_final: 0.6494 (pt0) REVERT: B 1 MET cc_start: 0.5706 (ppp) cc_final: 0.5413 (ppp) REVERT: B 32 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8226 (mmtm) REVERT: B 201 LYS cc_start: 0.7243 (mttt) cc_final: 0.6757 (mmtt) REVERT: B 467 ILE cc_start: 0.8835 (mm) cc_final: 0.8455 (mt) REVERT: B 505 LYS cc_start: 0.8555 (mmtp) cc_final: 0.8260 (mmmt) REVERT: B 512 ASP cc_start: 0.8295 (m-30) cc_final: 0.7836 (m-30) REVERT: B 517 MET cc_start: 0.8356 (mmm) cc_final: 0.7887 (mmm) outliers start: 36 outliers final: 21 residues processed: 161 average time/residue: 0.2181 time to fit residues: 46.1539 Evaluate side-chains 152 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 589 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7916 Z= 0.166 Angle : 0.501 5.470 10762 Z= 0.261 Chirality : 0.041 0.136 1246 Planarity : 0.004 0.042 1322 Dihedral : 5.741 77.912 1072 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.65 % Allowed : 11.69 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.27), residues: 976 helix: -0.45 (0.22), residues: 532 sheet: -0.97 (0.49), residues: 120 loop : -1.07 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 144 HIS 0.005 0.001 HIS A 57 PHE 0.008 0.001 PHE A 585 TYR 0.010 0.001 TYR B 617 ARG 0.004 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.907 Fit side-chains REVERT: A 1 MET cc_start: 0.5555 (ppp) cc_final: 0.5212 (ppp) REVERT: A 32 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8239 (mmtt) REVERT: A 201 LYS cc_start: 0.7242 (mttt) cc_final: 0.6801 (mmtt) REVERT: A 459 SER cc_start: 0.8565 (t) cc_final: 0.8245 (p) REVERT: A 467 ILE cc_start: 0.8819 (mm) cc_final: 0.8437 (mt) REVERT: A 505 LYS cc_start: 0.8558 (mmtp) cc_final: 0.8293 (mmmt) REVERT: A 512 ASP cc_start: 0.8209 (m-30) cc_final: 0.7942 (m-30) REVERT: A 517 MET cc_start: 0.8283 (mmm) cc_final: 0.7998 (mmm) REVERT: A 521 SER cc_start: 0.8167 (t) cc_final: 0.7945 (t) REVERT: D 56 GLN cc_start: 0.6747 (pt0) cc_final: 0.6493 (pt0) REVERT: B 1 MET cc_start: 0.5733 (ppp) cc_final: 0.5451 (ppp) REVERT: B 32 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8181 (mmtt) REVERT: B 201 LYS cc_start: 0.7240 (mttt) cc_final: 0.6777 (mmtt) REVERT: B 467 ILE cc_start: 0.8822 (mm) cc_final: 0.8429 (mt) REVERT: B 505 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8278 (mmmt) REVERT: B 512 ASP cc_start: 0.8255 (m-30) cc_final: 0.7998 (m-30) REVERT: B 517 MET cc_start: 0.8296 (mmm) cc_final: 0.7966 (mmm) REVERT: B 547 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8498 (tpm170) outliers start: 22 outliers final: 17 residues processed: 161 average time/residue: 0.2226 time to fit residues: 46.6355 Evaluate side-chains 161 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 589 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.0070 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 0.0270 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7916 Z= 0.133 Angle : 0.484 5.415 10762 Z= 0.252 Chirality : 0.041 0.138 1246 Planarity : 0.004 0.041 1322 Dihedral : 5.402 74.208 1072 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.01 % Allowed : 11.93 % Favored : 85.06 % 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: -0.72 (0.27), residues: 976 helix: -0.01 (0.23), residues: 530 sheet: -0.63 (0.50), residues: 120 loop : -0.97 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 144 HIS 0.004 0.001 HIS A 57 PHE 0.009 0.001 PHE A 585 TYR 0.009 0.001 TYR C 99 ARG 0.004 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 0.803 Fit side-chains REVERT: A 1 MET cc_start: 0.5574 (ppp) cc_final: 0.5366 (ppp) REVERT: A 32 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8213 (mmtt) REVERT: A 158 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7799 (ttmt) REVERT: A 201 LYS cc_start: 0.7102 (mttt) cc_final: 0.6691 (mmtt) REVERT: A 459 SER cc_start: 0.8591 (t) cc_final: 0.8263 (p) REVERT: A 467 ILE cc_start: 0.8783 (mm) cc_final: 0.8403 (mt) REVERT: A 505 LYS cc_start: 0.8519 (mmtp) cc_final: 0.8286 (mmmt) REVERT: A 512 ASP cc_start: 0.8069 (m-30) cc_final: 0.7749 (m-30) REVERT: A 517 MET cc_start: 0.8239 (mmm) cc_final: 0.7927 (mmm) REVERT: A 521 SER cc_start: 0.8056 (t) cc_final: 0.7845 (t) REVERT: A 547 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8411 (tpm170) REVERT: B 1 MET cc_start: 0.5656 (ppp) cc_final: 0.5416 (ppp) REVERT: B 32 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8188 (mmtt) REVERT: B 201 LYS cc_start: 0.7138 (mttt) cc_final: 0.6735 (mmtt) REVERT: B 467 ILE cc_start: 0.8787 (mm) cc_final: 0.8415 (mt) REVERT: B 505 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8298 (mmmt) REVERT: B 512 ASP cc_start: 0.8138 (m-30) cc_final: 0.7924 (m-30) REVERT: B 517 MET cc_start: 0.8234 (mmm) cc_final: 0.7914 (mmm) REVERT: B 547 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8473 (tpm170) outliers start: 25 outliers final: 21 residues processed: 159 average time/residue: 0.2519 time to fit residues: 51.0530 Evaluate side-chains 162 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 589 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 36 optimal weight: 0.2980 chunk 55 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7916 Z= 0.190 Angle : 0.505 5.482 10762 Z= 0.261 Chirality : 0.042 0.133 1246 Planarity : 0.004 0.042 1322 Dihedral : 5.403 74.601 1072 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.37 % Allowed : 12.17 % Favored : 84.46 % 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: -0.71 (0.27), residues: 976 helix: 0.06 (0.23), residues: 534 sheet: -0.74 (0.48), residues: 132 loop : -1.03 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 37 HIS 0.004 0.001 HIS A 57 PHE 0.007 0.001 PHE B 493 TYR 0.010 0.001 TYR C 99 ARG 0.006 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.922 Fit side-chains REVERT: A 1 MET cc_start: 0.5624 (ppp) cc_final: 0.5368 (ppp) REVERT: A 32 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8224 (mmtt) REVERT: A 459 SER cc_start: 0.8572 (t) cc_final: 0.8224 (p) REVERT: A 467 ILE cc_start: 0.8792 (mm) cc_final: 0.8419 (mt) REVERT: A 472 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8536 (mmtt) REVERT: A 505 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8355 (mmmt) REVERT: A 512 ASP cc_start: 0.8060 (m-30) cc_final: 0.7758 (m-30) REVERT: A 517 MET cc_start: 0.8290 (mmm) cc_final: 0.7993 (mmm) REVERT: A 547 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8397 (tpm170) REVERT: B 32 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8186 (mmtt) REVERT: B 201 LYS cc_start: 0.7144 (mttt) cc_final: 0.6744 (mmtt) REVERT: B 467 ILE cc_start: 0.8807 (mm) cc_final: 0.8436 (mt) REVERT: B 505 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8328 (mmmt) REVERT: B 512 ASP cc_start: 0.8142 (m-30) cc_final: 0.7905 (m-30) REVERT: B 517 MET cc_start: 0.8299 (mmm) cc_final: 0.8007 (mmm) REVERT: B 547 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8464 (tpm170) outliers start: 28 outliers final: 25 residues processed: 151 average time/residue: 0.2408 time to fit residues: 46.8872 Evaluate side-chains 158 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 589 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7916 Z= 0.182 Angle : 0.514 11.247 10762 Z= 0.261 Chirality : 0.042 0.130 1246 Planarity : 0.004 0.041 1322 Dihedral : 5.338 73.690 1072 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.01 % Allowed : 12.05 % Favored : 84.94 % 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 (0.27), residues: 976 helix: 0.16 (0.23), residues: 536 sheet: -0.65 (0.49), residues: 132 loop : -0.91 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 37 HIS 0.004 0.001 HIS A 57 PHE 0.007 0.001 PHE B 493 TYR 0.011 0.001 TYR C 99 ARG 0.006 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.883 Fit side-chains REVERT: A 1 MET cc_start: 0.5600 (ppp) cc_final: 0.5363 (ppp) REVERT: A 32 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8204 (mmtt) REVERT: A 459 SER cc_start: 0.8598 (t) cc_final: 0.8229 (p) REVERT: A 467 ILE cc_start: 0.8805 (mm) cc_final: 0.8431 (mt) REVERT: A 505 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8361 (mmmt) REVERT: A 512 ASP cc_start: 0.8049 (m-30) cc_final: 0.7725 (m-30) REVERT: A 517 MET cc_start: 0.8296 (mmm) cc_final: 0.7993 (mmm) REVERT: A 547 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8377 (tpm170) REVERT: B 32 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8173 (mmtt) REVERT: B 201 LYS cc_start: 0.7200 (mttt) cc_final: 0.6790 (mmtt) REVERT: B 467 ILE cc_start: 0.8804 (mm) cc_final: 0.8430 (mt) REVERT: B 505 LYS cc_start: 0.8582 (mmtp) cc_final: 0.8306 (mmmt) REVERT: B 512 ASP cc_start: 0.8153 (m-30) cc_final: 0.7800 (m-30) REVERT: B 517 MET cc_start: 0.8276 (mmm) cc_final: 0.7951 (mmm) REVERT: B 547 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8440 (tpm170) outliers start: 25 outliers final: 22 residues processed: 148 average time/residue: 0.2437 time to fit residues: 46.4867 Evaluate side-chains 155 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.0270 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7916 Z= 0.197 Angle : 0.518 9.882 10762 Z= 0.263 Chirality : 0.042 0.135 1246 Planarity : 0.004 0.040 1322 Dihedral : 5.317 73.357 1072 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.01 % Allowed : 11.81 % Favored : 85.18 % 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: -0.46 (0.27), residues: 976 helix: 0.23 (0.23), residues: 536 sheet: -0.65 (0.48), residues: 132 loop : -0.87 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 37 HIS 0.004 0.001 HIS A 57 PHE 0.007 0.001 PHE B 493 TYR 0.011 0.001 TYR C 99 ARG 0.005 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.835 Fit side-chains REVERT: A 1 MET cc_start: 0.5691 (ppp) cc_final: 0.5379 (ppp) REVERT: A 32 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8197 (mmtt) REVERT: A 459 SER cc_start: 0.8564 (t) cc_final: 0.8199 (p) REVERT: A 467 ILE cc_start: 0.8806 (mm) cc_final: 0.8432 (mt) REVERT: A 472 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8602 (mmtt) REVERT: A 505 LYS cc_start: 0.8547 (mmtp) cc_final: 0.8302 (mmmt) REVERT: A 512 ASP cc_start: 0.8102 (m-30) cc_final: 0.7767 (m-30) REVERT: A 517 MET cc_start: 0.8303 (mmm) cc_final: 0.7995 (mmm) REVERT: A 547 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8368 (tpm170) REVERT: B 32 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8194 (mmtt) REVERT: B 201 LYS cc_start: 0.7238 (mttt) cc_final: 0.6861 (mmtt) REVERT: B 467 ILE cc_start: 0.8807 (mm) cc_final: 0.8442 (mt) REVERT: B 505 LYS cc_start: 0.8547 (mmtp) cc_final: 0.8291 (mmmt) REVERT: B 512 ASP cc_start: 0.8100 (m-30) cc_final: 0.7768 (m-30) REVERT: B 517 MET cc_start: 0.8308 (mmm) cc_final: 0.7998 (mmm) REVERT: B 547 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8446 (tpm170) outliers start: 25 outliers final: 23 residues processed: 148 average time/residue: 0.2384 time to fit residues: 45.4710 Evaluate side-chains 156 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0170 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7916 Z= 0.142 Angle : 0.491 9.373 10762 Z= 0.251 Chirality : 0.041 0.130 1246 Planarity : 0.004 0.040 1322 Dihedral : 5.069 69.646 1072 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.65 % Allowed : 12.53 % Favored : 84.82 % 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: -0.17 (0.27), residues: 976 helix: 0.49 (0.23), residues: 538 sheet: -0.57 (0.48), residues: 132 loop : -0.78 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 37 HIS 0.004 0.001 HIS A 57 PHE 0.006 0.001 PHE B 585 TYR 0.009 0.001 TYR C 99 ARG 0.006 0.000 ARG B 565 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 0.916 Fit side-chains REVERT: A 1 MET cc_start: 0.5672 (ppp) cc_final: 0.5372 (ppp) REVERT: A 32 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8143 (mmtt) REVERT: A 459 SER cc_start: 0.8599 (t) cc_final: 0.8237 (p) REVERT: A 467 ILE cc_start: 0.8801 (mm) cc_final: 0.8426 (mt) REVERT: A 472 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8535 (mmtt) REVERT: A 505 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8306 (mmmt) REVERT: A 512 ASP cc_start: 0.7955 (m-30) cc_final: 0.7660 (m-30) REVERT: A 547 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7796 (tpt90) REVERT: B 32 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8150 (mmtt) REVERT: B 505 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8302 (mmmt) REVERT: B 512 ASP cc_start: 0.7956 (m-30) cc_final: 0.7668 (m-30) outliers start: 22 outliers final: 20 residues processed: 148 average time/residue: 0.2582 time to fit residues: 49.6233 Evaluate side-chains 153 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.184998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129115 restraints weight = 8801.227| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.06 r_work: 0.2964 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7916 Z= 0.191 Angle : 0.532 9.024 10762 Z= 0.267 Chirality : 0.042 0.132 1246 Planarity : 0.004 0.039 1322 Dihedral : 5.138 70.606 1072 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.77 % Allowed : 12.29 % Favored : 84.94 % 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: -0.24 (0.28), residues: 976 helix: 0.52 (0.23), residues: 538 sheet: -1.21 (0.45), residues: 156 loop : -0.58 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 63 HIS 0.004 0.001 HIS B 57 PHE 0.007 0.001 PHE B 493 TYR 0.011 0.001 TYR C 99 ARG 0.005 0.000 ARG B 565 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.43 seconds wall clock time: 38 minutes 1.43 seconds (2281.43 seconds total)