Starting phenix.real_space_refine on Mon Mar 18 09:39:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/03_2024/7lyb_23591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/03_2024/7lyb_23591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/03_2024/7lyb_23591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/03_2024/7lyb_23591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/03_2024/7lyb_23591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/03_2024/7lyb_23591.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 293 5.49 5 S 42 5.16 5 C 8325 2.51 5 N 2730 2.21 5 O 3305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "M GLU 9": "OE1" <-> "OE2" Residue "N GLU 45": "OE1" <-> "OE2" Residue "N GLU 59": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14699 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "M" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "P" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1172 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "N" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10581 SG CYS M 24 43.868 68.900 51.864 1.00119.93 S ATOM 10602 SG CYS M 27 44.034 71.422 49.323 1.00122.99 S ATOM 10738 SG CYS M 44 44.128 67.724 48.466 1.00120.03 S ATOM 10764 SG CYS M 47 47.166 69.234 50.677 1.00121.01 S ATOM 10695 SG CYS M 39 49.322 59.427 59.192 1.00105.98 S ATOM 10872 SG CYS M 61 49.091 63.127 60.251 1.00109.94 S ATOM 10893 SG CYS M 64 48.032 60.263 62.662 1.00113.55 S ATOM 12486 SG CYS N 50 39.500 41.325 49.940 1.00121.58 S ATOM 12509 SG CYS N 53 37.412 38.399 51.757 1.00124.96 S ATOM 12646 SG CYS N 71 37.226 41.341 52.330 1.00123.85 S ATOM 12666 SG CYS N 74 40.950 38.797 52.718 1.00122.85 S ATOM 12602 SG CYS N 66 50.300 46.406 49.328 1.00 97.99 S ATOM 12722 SG CYS N 83 49.746 42.722 48.383 1.00 96.27 S ATOM 12742 SG CYS N 86 51.078 45.165 45.752 1.00 92.11 S Time building chain proxies: 8.18, per 1000 atoms: 0.56 Number of scatterers: 14699 At special positions: 0 Unit cell: (127.844, 124.751, 119.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 42 16.00 P 293 15.00 O 3305 8.00 N 2730 7.00 C 8325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.65 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 47 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 41 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 61 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 64 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 50 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 53 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 71 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 74 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" ND1 HIS N 68 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 86 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 83 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 66 " Number of angles added : 18 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 63.3% alpha, 4.0% beta 139 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.554A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.803A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.636A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.820A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.829A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.555A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.803A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.580A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.640A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.585A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 22 removed outlier: 3.699A pdb=" N VAL M 11 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN M 19 " --> pdb=" O ILE M 15 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS M 20 " --> pdb=" O ASN M 16 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'M' and resid 79 through 97 removed outlier: 3.686A pdb=" N PHE M 93 " --> pdb=" O ILE M 89 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN M 94 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 86 through 91 Processing helix chain 'P' and resid 98 through 112 Processing helix chain 'P' and resid 120 through 130 removed outlier: 3.707A pdb=" N ALA P 124 " --> pdb=" O VAL P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 147 Processing helix chain 'N' and resid 34 through 46 removed outlier: 3.625A pdb=" N LEU N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 76 Processing helix chain 'N' and resid 98 through 116 removed outlier: 3.695A pdb=" N ILE N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.554A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.548A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.507A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.528A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.936A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.333A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.101A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.375A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 35 through 36 removed outlier: 3.683A pdb=" N GLN M 74 " --> pdb=" O SER M 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'P' and resid 21 through 25 Processing sheet with id=AB5, first strand: chain 'N' and resid 60 through 61 507 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2054 1.32 - 1.45: 5338 1.45 - 1.57: 7525 1.57 - 1.69: 584 1.69 - 1.81: 58 Bond restraints: 15559 Sorted by residual: bond pdb=" C MET E 90 " pdb=" O MET E 90 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.19e-02 7.06e+03 5.01e+00 bond pdb=" CG ARG H 33 " pdb=" CD ARG H 33 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C MET A 90 " pdb=" O MET A 90 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.19e-02 7.06e+03 3.74e+00 bond pdb=" C6 DG J -36 " pdb=" O6 DG J -36 " ideal model delta sigma weight residual 1.239 1.203 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " ideal model delta sigma weight residual 1.326 1.308 0.018 1.10e-02 8.26e+03 2.63e+00 ... (remaining 15554 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.07: 1299 105.07 - 112.29: 8536 112.29 - 119.51: 4827 119.51 - 126.72: 6745 126.72 - 133.94: 864 Bond angle restraints: 22271 Sorted by residual: angle pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " pdb=" NH1 ARG H 33 " ideal model delta sigma weight residual 121.50 118.14 3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" CA ARG A 134 " pdb=" CB ARG A 134 " pdb=" CG ARG A 134 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA ARG E 134 " pdb=" CB ARG E 134 " pdb=" CG ARG E 134 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA ARG H 33 " pdb=" CB ARG H 33 " pdb=" CG ARG H 33 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB ARG H 33 " pdb=" CG ARG H 33 " pdb=" CD ARG H 33 " ideal model delta sigma weight residual 111.30 103.78 7.52 2.30e+00 1.89e-01 1.07e+01 ... (remaining 22266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.21: 6984 31.21 - 62.42: 1639 62.42 - 93.63: 39 93.63 - 124.84: 0 124.84 - 156.05: 2 Dihedral angle restraints: 8664 sinusoidal: 5478 harmonic: 3186 Sorted by residual: dihedral pdb=" CA CYS M 64 " pdb=" C CYS M 64 " pdb=" N LYS M 65 " pdb=" CA LYS M 65 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 63.95 156.05 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 68.67 151.33 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 8661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1866 0.044 - 0.087: 515 0.087 - 0.131: 129 0.131 - 0.175: 17 0.175 - 0.218: 3 Chirality restraints: 2530 Sorted by residual: chirality pdb=" CG LEU F 62 " pdb=" CB LEU F 62 " pdb=" CD1 LEU F 62 " pdb=" CD2 LEU F 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB THR G 101 " pdb=" CA THR G 101 " pdb=" OG1 THR G 101 " pdb=" CG2 THR G 101 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LYS G 118 " pdb=" N LYS G 118 " pdb=" C LYS G 118 " pdb=" CB LYS G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2527 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 35 " -0.037 2.00e-02 2.50e+03 3.29e-02 2.44e+01 pdb=" N1 DC I 35 " 0.058 2.00e-02 2.50e+03 pdb=" C2 DC I 35 " 0.020 2.00e-02 2.50e+03 pdb=" O2 DC I 35 " -0.026 2.00e-02 2.50e+03 pdb=" N3 DC I 35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 35 " 0.045 2.00e-02 2.50e+03 pdb=" N4 DC I 35 " -0.040 2.00e-02 2.50e+03 pdb=" C5 DC I 35 " -0.013 2.00e-02 2.50e+03 pdb=" C6 DC I 35 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -9 " -0.038 2.00e-02 2.50e+03 3.17e-02 2.27e+01 pdb=" N1 DC J -9 " 0.078 2.00e-02 2.50e+03 pdb=" C2 DC J -9 " -0.037 2.00e-02 2.50e+03 pdb=" O2 DC J -9 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DC J -9 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC J -9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J -9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC J -9 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC J -9 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -36 " 0.017 2.00e-02 2.50e+03 2.46e-02 1.82e+01 pdb=" N9 DG J -36 " -0.030 2.00e-02 2.50e+03 pdb=" C8 DG J -36 " 0.022 2.00e-02 2.50e+03 pdb=" N7 DG J -36 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG J -36 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -36 " -0.048 2.00e-02 2.50e+03 pdb=" O6 DG J -36 " 0.039 2.00e-02 2.50e+03 pdb=" N1 DG J -36 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG J -36 " -0.027 2.00e-02 2.50e+03 pdb=" N2 DG J -36 " 0.031 2.00e-02 2.50e+03 pdb=" N3 DG J -36 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG J -36 " -0.000 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 2130 2.76 - 3.47: 19113 3.47 - 4.19: 39591 4.19 - 4.90: 60644 Nonbonded interactions: 121480 Sorted by model distance: nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.330 3.350 nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.331 3.350 nonbonded pdb=" NH2 ARG H 33 " pdb=" OP1 DA I 50 " model vdw 2.096 2.520 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.122 2.496 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.126 2.440 ... (remaining 121475 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 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = (chain 'F' and (resid 23 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and resid 31 through 123) selection = chain 'H' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.380 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 48.600 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.006 0.066 15559 Z= 0.347 Angle : 0.732 8.091 22271 Z= 0.437 Chirality : 0.043 0.218 2530 Planarity : 0.005 0.040 1810 Dihedral : 26.071 156.048 6600 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.02 (0.24), residues: 1074 helix: 0.31 (0.19), residues: 651 sheet: -1.28 (0.98), residues: 22 loop : -2.31 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 141 HIS 0.011 0.002 HIS A 39 PHE 0.027 0.002 PHE C 25 TYR 0.022 0.002 TYR C 57 ARG 0.007 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8392 (mmt-90) cc_final: 0.8186 (mpt90) REVERT: D 90 THR cc_start: 0.8819 (p) cc_final: 0.8280 (p) REVERT: M 14 VAL cc_start: 0.8994 (t) cc_final: 0.8684 (t) REVERT: M 15 ILE cc_start: 0.8663 (pt) cc_final: 0.8315 (pt) REVERT: M 21 ILE cc_start: 0.8810 (mm) cc_final: 0.8471 (mm) REVERT: C 95 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8679 (ttmm) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.3765 time to fit residues: 154.0633 Evaluate side-chains 249 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 40.0000 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 113 HIS B 25 ASN D 47 GLN F 27 GLN F 64 ASN H 84 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN N 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15559 Z= 0.315 Angle : 0.633 6.812 22271 Z= 0.367 Chirality : 0.038 0.153 2530 Planarity : 0.005 0.035 1810 Dihedral : 28.878 157.401 4409 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.70 % Allowed : 11.82 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.83 (0.26), residues: 1074 helix: 1.94 (0.20), residues: 672 sheet: 0.79 (1.17), residues: 22 loop : -2.15 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 93 HIS 0.009 0.002 HIS B 75 PHE 0.019 0.002 PHE N 70 TYR 0.019 0.002 TYR D 83 ARG 0.008 0.001 ARG N 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 272 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.8669 (tpp) cc_final: 0.8430 (tmm) REVERT: D 86 ARG cc_start: 0.8368 (mmt-90) cc_final: 0.8105 (mpt180) REVERT: D 90 THR cc_start: 0.8767 (p) cc_final: 0.8542 (p) REVERT: H 71 GLU cc_start: 0.7616 (tp30) cc_final: 0.7382 (tp30) REVERT: M 32 LYS cc_start: 0.6390 (mttt) cc_final: 0.6134 (ptpt) REVERT: N 62 CYS cc_start: 0.8171 (t) cc_final: 0.7897 (t) outliers start: 16 outliers final: 13 residues processed: 279 average time/residue: 0.3290 time to fit residues: 124.2776 Evaluate side-chains 256 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain C residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 30.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN M 12 GLN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15559 Z= 0.200 Angle : 0.572 8.081 22271 Z= 0.335 Chirality : 0.035 0.155 2530 Planarity : 0.004 0.035 1810 Dihedral : 28.569 159.384 4409 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.81 % Allowed : 15.76 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.46 (0.27), residues: 1074 helix: 2.38 (0.20), residues: 676 sheet: 1.42 (1.25), residues: 22 loop : -1.87 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 93 HIS 0.008 0.001 HIS P 32 PHE 0.012 0.001 PHE N 70 TYR 0.026 0.002 TYR H 83 ARG 0.007 0.000 ARG M 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 274 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 15 ILE cc_start: 0.8379 (pt) cc_final: 0.8140 (pt) REVERT: M 45 LYS cc_start: 0.8689 (tmmt) cc_final: 0.8318 (tmmt) REVERT: P 34 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6708 (tp40) outliers start: 17 outliers final: 11 residues processed: 284 average time/residue: 0.3345 time to fit residues: 129.0383 Evaluate side-chains 258 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 247 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN H 84 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15559 Z= 0.173 Angle : 0.556 8.581 22271 Z= 0.326 Chirality : 0.034 0.160 2530 Planarity : 0.004 0.035 1810 Dihedral : 28.468 160.088 4409 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.66 % Allowed : 16.40 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.76 (0.27), residues: 1074 helix: 2.53 (0.20), residues: 676 sheet: 1.99 (1.20), residues: 21 loop : -1.59 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 33 HIS 0.006 0.001 HIS B 75 PHE 0.013 0.001 PHE N 70 TYR 0.037 0.002 TYR D 83 ARG 0.006 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 42 TYR cc_start: 0.8064 (t80) cc_final: 0.7790 (t80) REVERT: M 15 ILE cc_start: 0.8260 (pt) cc_final: 0.7924 (pt) outliers start: 25 outliers final: 15 residues processed: 283 average time/residue: 0.3243 time to fit residues: 125.0708 Evaluate side-chains 264 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 0.0370 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN M 12 GLN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15559 Z= 0.354 Angle : 0.625 8.288 22271 Z= 0.360 Chirality : 0.038 0.153 2530 Planarity : 0.004 0.032 1810 Dihedral : 28.784 161.235 4409 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.09 % Allowed : 18.21 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.73 (0.27), residues: 1074 helix: 2.56 (0.20), residues: 674 sheet: 1.54 (1.20), residues: 21 loop : -1.67 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 33 HIS 0.007 0.001 HIS B 75 PHE 0.013 0.001 PHE N 70 TYR 0.054 0.002 TYR D 83 ARG 0.005 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 15 ILE cc_start: 0.8072 (pt) cc_final: 0.7819 (pt) REVERT: M 88 LYS cc_start: 0.8689 (mttp) cc_final: 0.8323 (tmmt) REVERT: P 147 MET cc_start: 0.4750 (mtm) cc_final: 0.4542 (mtm) REVERT: N 46 LYS cc_start: 0.8830 (pttt) cc_final: 0.8595 (ptpp) outliers start: 29 outliers final: 24 residues processed: 252 average time/residue: 0.3245 time to fit residues: 111.0800 Evaluate side-chains 255 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN H 47 GLN H 84 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15559 Z= 0.190 Angle : 0.573 9.257 22271 Z= 0.335 Chirality : 0.035 0.165 2530 Planarity : 0.004 0.035 1810 Dihedral : 28.566 161.564 4409 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.34 % Allowed : 19.49 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.88 (0.27), residues: 1074 helix: 2.63 (0.20), residues: 675 sheet: 1.49 (1.20), residues: 21 loop : -1.49 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 93 HIS 0.006 0.001 HIS P 32 PHE 0.014 0.001 PHE N 70 TYR 0.034 0.001 TYR B 88 ARG 0.007 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 254 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 88 LYS cc_start: 0.8673 (mttp) cc_final: 0.8326 (tmmt) outliers start: 22 outliers final: 16 residues processed: 265 average time/residue: 0.3344 time to fit residues: 119.5140 Evaluate side-chains 264 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 248 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN H 84 ASN ** P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 HIS ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 15559 Z= 0.439 Angle : 0.680 9.195 22271 Z= 0.388 Chirality : 0.041 0.169 2530 Planarity : 0.004 0.032 1810 Dihedral : 29.011 162.573 4409 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.30 % Allowed : 20.34 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.60 (0.27), residues: 1074 helix: 2.46 (0.20), residues: 673 sheet: 1.21 (1.22), residues: 21 loop : -1.68 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 33 HIS 0.011 0.002 HIS N 116 PHE 0.015 0.002 PHE N 70 TYR 0.053 0.003 TYR B 88 ARG 0.006 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 GLU cc_start: 0.7678 (mp0) cc_final: 0.7422 (mp0) REVERT: H 33 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6895 (tpt170) REVERT: M 42 ILE cc_start: 0.8743 (mm) cc_final: 0.8446 (mm) REVERT: M 88 LYS cc_start: 0.8675 (mttp) cc_final: 0.8367 (ttpt) REVERT: N 46 LYS cc_start: 0.8843 (pttt) cc_final: 0.8572 (ptpp) outliers start: 31 outliers final: 21 residues processed: 252 average time/residue: 0.3664 time to fit residues: 124.0233 Evaluate side-chains 254 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 232 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN F 27 GLN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15559 Z= 0.182 Angle : 0.583 8.939 22271 Z= 0.341 Chirality : 0.035 0.159 2530 Planarity : 0.004 0.037 1810 Dihedral : 28.627 163.410 4409 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.92 % Allowed : 21.51 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.90 (0.27), residues: 1074 helix: 2.63 (0.20), residues: 672 sheet: 1.34 (1.23), residues: 21 loop : -1.41 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 93 HIS 0.007 0.001 HIS N 116 PHE 0.014 0.001 PHE N 70 TYR 0.058 0.002 TYR B 88 ARG 0.006 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 ILE cc_start: 0.8737 (mm) cc_final: 0.8324 (mm) REVERT: N 46 LYS cc_start: 0.8822 (pttt) cc_final: 0.8560 (ptpp) REVERT: N 62 CYS cc_start: 0.8239 (t) cc_final: 0.8006 (t) REVERT: C 11 SER cc_start: 0.7387 (t) cc_final: 0.7096 (p) outliers start: 18 outliers final: 16 residues processed: 263 average time/residue: 0.3318 time to fit residues: 117.6252 Evaluate side-chains 259 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 243 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN H 84 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15559 Z= 0.195 Angle : 0.590 10.317 22271 Z= 0.342 Chirality : 0.035 0.182 2530 Planarity : 0.004 0.057 1810 Dihedral : 28.700 163.437 4409 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.81 % Allowed : 22.04 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.92 (0.27), residues: 1074 helix: 2.62 (0.20), residues: 674 sheet: 0.99 (1.26), residues: 22 loop : -1.34 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 93 HIS 0.007 0.001 HIS N 116 PHE 0.013 0.001 PHE N 70 TYR 0.058 0.002 TYR B 88 ARG 0.009 0.000 ARG N 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 14 VAL cc_start: 0.9151 (t) cc_final: 0.8898 (t) REVERT: M 42 ILE cc_start: 0.8682 (mm) cc_final: 0.8322 (mm) REVERT: N 62 CYS cc_start: 0.8254 (t) cc_final: 0.7957 (t) REVERT: C 11 SER cc_start: 0.7694 (t) cc_final: 0.7381 (p) outliers start: 17 outliers final: 16 residues processed: 254 average time/residue: 0.3311 time to fit residues: 113.7903 Evaluate side-chains 259 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 243 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15559 Z= 0.381 Angle : 0.666 10.264 22271 Z= 0.379 Chirality : 0.039 0.209 2530 Planarity : 0.004 0.033 1810 Dihedral : 29.083 164.944 4409 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.92 % Allowed : 21.51 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.69 (0.27), residues: 1074 helix: 2.44 (0.20), residues: 675 sheet: 0.01 (1.18), residues: 24 loop : -1.39 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 91 HIS 0.007 0.002 HIS H 82 PHE 0.014 0.002 PHE N 70 TYR 0.076 0.003 TYR F 88 ARG 0.010 0.001 ARG N 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7836 (t0) cc_final: 0.7491 (t0) REVERT: M 42 ILE cc_start: 0.8681 (mm) cc_final: 0.8381 (mm) REVERT: M 46 PHE cc_start: 0.8294 (t80) cc_final: 0.8070 (t80) REVERT: N 62 CYS cc_start: 0.8326 (t) cc_final: 0.8051 (t) outliers start: 18 outliers final: 18 residues processed: 243 average time/residue: 0.3411 time to fit residues: 111.4908 Evaluate side-chains 247 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 229 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 47 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 56 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.087983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.052742 restraints weight = 42961.340| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.68 r_work: 0.2597 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15559 Z= 0.191 Angle : 0.610 10.241 22271 Z= 0.350 Chirality : 0.035 0.182 2530 Planarity : 0.004 0.036 1810 Dihedral : 28.710 165.808 4409 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.92 % Allowed : 22.26 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.91 (0.27), residues: 1074 helix: 2.57 (0.20), residues: 672 sheet: 0.37 (1.24), residues: 24 loop : -1.19 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 93 HIS 0.006 0.001 HIS H 82 PHE 0.013 0.001 PHE N 70 TYR 0.061 0.002 TYR F 88 ARG 0.009 0.000 ARG N 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3186.74 seconds wall clock time: 57 minutes 38.43 seconds (3458.43 seconds total)