Starting phenix.real_space_refine (version: dev) on Sat Feb 18 08:36:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2023/7y9v_33693_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2023/7y9v_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_2023/7y9v_33693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2023/7y9v_33693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2023/7y9v_33693_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9v_33693/02_2023/7y9v_33693_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.68, per 1000 atoms: 0.61 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: 2.83 Conformation dependent library (CDL) restraints added in 1.1 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: 0.78 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: 2.22 Time building geometry restraints manager: 3.04 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 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. 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: 0.820 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: 4.410 Check model and map are aligned: 0.120 Process input model: 22.590 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 % 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 *********************** 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 : 0.875 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.2672 time to fit residues: 63.4790 Evaluate side-chains 117 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 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: 0.6980 ------------------------------------------------------------------------------- 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: 0.8280 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7916 Z= 0.201 Angle : 0.606 6.600 10762 Z= 0.318 Chirality : 0.043 0.174 1246 Planarity : 0.006 0.050 1322 Dihedral : 6.703 83.343 1072 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.45 % 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: -3.83 (0.23), residues: 976 helix: -2.65 (0.17), residues: 542 sheet: -2.12 (0.45), residues: 120 loop : -2.03 (0.32), residues: 314 *********************** 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 170 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 0.881 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 166 average time/residue: 0.2088 time to fit residues: 46.9196 Evaluate side-chains 128 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0712 time to fit residues: 2.1134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 7916 Z= 0.327 Angle : 0.618 8.552 10762 Z= 0.317 Chirality : 0.045 0.176 1246 Planarity : 0.005 0.045 1322 Dihedral : 6.363 80.810 1072 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.71 (0.25), residues: 976 helix: -1.58 (0.20), residues: 536 sheet: -1.96 (0.44), residues: 138 loop : -1.66 (0.34), residues: 302 *********************** 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 142 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.922 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 136 average time/residue: 0.1833 time to fit residues: 34.7659 Evaluate side-chains 128 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0765 time to fit residues: 2.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7916 Z= 0.259 Angle : 0.564 5.605 10762 Z= 0.292 Chirality : 0.044 0.173 1246 Planarity : 0.005 0.044 1322 Dihedral : 6.076 80.480 1072 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.79 (0.26), residues: 976 helix: -0.92 (0.22), residues: 532 sheet: -1.21 (0.50), residues: 118 loop : -1.32 (0.34), residues: 326 *********************** 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 148 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.834 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 142 average time/residue: 0.2009 time to fit residues: 39.0707 Evaluate side-chains 130 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1879 time to fit residues: 3.4209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.3254 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= 0.189 Angle : 0.541 8.292 10762 Z= 0.275 Chirality : 0.042 0.164 1246 Planarity : 0.004 0.042 1322 Dihedral : 5.777 77.453 1072 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.27), residues: 976 helix: -0.51 (0.22), residues: 532 sheet: -0.93 (0.51), residues: 118 loop : -1.05 (0.35), residues: 326 *********************** 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 130 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.918 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 126 average time/residue: 0.1969 time to fit residues: 34.2261 Evaluate side-chains 121 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0878 time to fit residues: 1.8470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0170 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.0870 overall best weight: 0.2354 ------------------------------------------------------------------------------- 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: 0.8266 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7916 Z= 0.127 Angle : 0.496 7.068 10762 Z= 0.254 Chirality : 0.041 0.163 1246 Planarity : 0.004 0.041 1322 Dihedral : 5.369 72.359 1072 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 976 helix: -0.06 (0.23), residues: 528 sheet: -0.69 (0.50), residues: 120 loop : -0.97 (0.35), residues: 328 *********************** 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 129 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.880 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 127 average time/residue: 0.2029 time to fit residues: 35.5130 Evaluate side-chains 122 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0797 time to fit residues: 1.7906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** D 78 ASN B 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 7916 Z= 0.407 Angle : 0.625 6.328 10762 Z= 0.319 Chirality : 0.047 0.171 1246 Planarity : 0.005 0.042 1322 Dihedral : 5.903 79.196 1072 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.27), residues: 976 helix: -0.41 (0.22), residues: 536 sheet: -1.54 (0.44), residues: 154 loop : -0.87 (0.37), residues: 286 *********************** 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 117 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.987 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 115 average time/residue: 0.1920 time to fit residues: 30.7770 Evaluate side-chains 113 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0819 time to fit residues: 1.6760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8322 moved from start: 0.3610 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= 0.203 Angle : 0.538 9.555 10762 Z= 0.273 Chirality : 0.042 0.157 1246 Planarity : 0.004 0.042 1322 Dihedral : 5.571 75.090 1072 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.84 % 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: -0.88 (0.27), residues: 976 helix: -0.04 (0.23), residues: 530 sheet: -1.49 (0.44), residues: 156 loop : -0.74 (0.37), residues: 290 *********************** 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 116 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.887 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 113 average time/residue: 0.2134 time to fit residues: 32.8133 Evaluate side-chains 115 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0828 time to fit residues: 2.2204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 7916 Z= 0.297 Angle : 0.587 8.864 10762 Z= 0.297 Chirality : 0.044 0.159 1246 Planarity : 0.005 0.042 1322 Dihedral : 5.654 75.908 1072 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.27), residues: 976 helix: -0.09 (0.22), residues: 530 sheet: -0.87 (0.48), residues: 130 loop : -0.90 (0.35), residues: 316 *********************** 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 109 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.918 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 108 average time/residue: 0.2012 time to fit residues: 30.3816 Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0732 time to fit residues: 1.3500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8314 moved from start: 0.3788 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= 0.188 Angle : 0.530 8.397 10762 Z= 0.270 Chirality : 0.042 0.157 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.361 71.820 1072 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.00 % 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: -0.52 (0.27), residues: 976 helix: 0.23 (0.23), residues: 530 sheet: -0.83 (0.47), residues: 132 loop : -0.87 (0.35), residues: 314 ********************** 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 112 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.904 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2055 time to fit residues: 31.4124 Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.181552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130185 restraints weight = 8795.750| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.14 r_work: 0.2986 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3860 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 : 0.546 10.244 10762 Z= 0.273 Chirality : 0.042 0.161 1246 Planarity : 0.004 0.042 1322 Dihedral : 5.245 70.345 1072 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.00 % 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 (0.27), residues: 976 helix: 0.42 (0.23), residues: 530 sheet: -0.81 (0.47), residues: 132 loop : -0.82 (0.35), residues: 314 =============================================================================== Job complete usr+sys time: 1843.45 seconds wall clock time: 34 minutes 14.92 seconds (2054.92 seconds total)