Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 07:21:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/10_2023/7lyb_23591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/10_2023/7lyb_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_23591/10_2023/7lyb_23591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/10_2023/7lyb_23591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/10_2023/7lyb_23591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyb_23591/10_2023/7lyb_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-1.21rc1-5097/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: 7.63, per 1000 atoms: 0.52 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: 6.96 Conformation dependent library (CDL) restraints added in 1.5 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: 6.88 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: 5.13 Time building geometry restraints manager: 7.43 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: 6773 31.21 - 62.42: 1594 62.42 - 93.63: 39 93.63 - 124.84: 0 124.84 - 156.05: 2 Dihedral angle restraints: 8408 sinusoidal: 5222 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 8405 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 4.320 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 47.100 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.270 ------------------------------------------------------------------------------- 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 : 26.168 156.048 6344 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 *********************** 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 : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.3921 time to fit residues: 161.0977 Evaluate side-chains 248 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5307 ------------------------------------------------------------------------------- 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: 1.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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: 0.8503 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15559 Z= 0.335 Angle : 0.647 8.576 22271 Z= 0.373 Chirality : 0.038 0.153 2530 Planarity : 0.004 0.035 1810 Dihedral : 29.374 156.797 4153 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.70 % Allowed : 12.35 % Favored : 85.94 % 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: 0.80 (0.26), residues: 1074 helix: 1.92 (0.20), residues: 672 sheet: 0.67 (1.14), residues: 22 loop : -2.18 (0.28), residues: 380 *********************** 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 281 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 265 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 271 average time/residue: 0.3401 time to fit residues: 124.4355 Evaluate side-chains 255 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 243 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1316 time to fit residues: 4.4157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 96 optimal weight: 30.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 G 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15559 Z= 0.252 Angle : 0.588 7.855 22271 Z= 0.343 Chirality : 0.036 0.163 2530 Planarity : 0.004 0.035 1810 Dihedral : 29.152 159.901 4153 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.60 % Allowed : 15.55 % Favored : 82.85 % 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: 1.37 (0.27), residues: 1074 helix: 2.34 (0.20), residues: 676 sheet: 1.25 (1.24), residues: 22 loop : -1.97 (0.29), residues: 376 *********************** 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 279 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 264 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 274 average time/residue: 0.3285 time to fit residues: 122.2947 Evaluate side-chains 256 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 245 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1536 time to fit residues: 4.3883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0030 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 0.0570 chunk 114 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3017 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= 0.181 Angle : 0.560 8.579 22271 Z= 0.329 Chirality : 0.034 0.161 2530 Planarity : 0.004 0.037 1810 Dihedral : 28.987 160.698 4153 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.49 % Allowed : 16.61 % Favored : 81.90 % 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: 1.74 (0.27), residues: 1074 helix: 2.61 (0.20), residues: 675 sheet: 1.52 (1.28), residues: 22 loop : -1.75 (0.30), residues: 377 *********************** 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 291 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 277 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 280 average time/residue: 0.3383 time to fit residues: 128.1454 Evaluate side-chains 254 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 247 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1344 time to fit residues: 3.2560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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** P 55 HIS G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15559 Z= 0.291 Angle : 0.602 8.880 22271 Z= 0.348 Chirality : 0.036 0.167 2530 Planarity : 0.004 0.034 1810 Dihedral : 29.143 161.271 4153 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.81 % Allowed : 18.64 % Favored : 79.55 % 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: 1.82 (0.27), residues: 1074 helix: 2.64 (0.20), residues: 676 sheet: -0.26 (1.07), residues: 32 loop : -1.55 (0.31), residues: 366 *********************** 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 264 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 247 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 257 average time/residue: 0.3376 time to fit residues: 117.3893 Evaluate side-chains 248 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 239 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1260 time to fit residues: 3.5332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15559 Z= 0.279 Angle : 0.610 9.029 22271 Z= 0.351 Chirality : 0.036 0.171 2530 Planarity : 0.004 0.035 1810 Dihedral : 29.180 161.888 4153 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.28 % Allowed : 19.91 % Favored : 78.81 % 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: 1.85 (0.27), residues: 1074 helix: 2.64 (0.20), residues: 677 sheet: -0.34 (1.05), residues: 32 loop : -1.50 (0.32), residues: 365 *********************** 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 263 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 256 average time/residue: 0.3436 time to fit residues: 118.7805 Evaluate side-chains 246 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1778 time to fit residues: 3.0799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 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: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15559 Z= 0.316 Angle : 0.631 10.689 22271 Z= 0.363 Chirality : 0.038 0.188 2530 Planarity : 0.004 0.034 1810 Dihedral : 29.302 162.758 4153 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.96 % Allowed : 21.19 % Favored : 77.85 % 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: 1.83 (0.27), residues: 1074 helix: 2.61 (0.20), residues: 675 sheet: 1.22 (1.23), residues: 22 loop : -1.53 (0.31), residues: 377 *********************** 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 251 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 242 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 246 average time/residue: 0.3884 time to fit residues: 128.9045 Evaluate side-chains 239 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2144 time to fit residues: 2.9132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2105 > 50: distance: 41 - 60: 27.606 distance: 46 - 67: 33.550 distance: 53 - 78: 30.101 distance: 57 - 60: 28.429 distance: 58 - 86: 37.388 distance: 60 - 61: 61.937 distance: 61 - 62: 56.085 distance: 61 - 64: 55.809 distance: 62 - 63: 43.442 distance: 62 - 67: 42.950 distance: 63 - 94: 60.338 distance: 64 - 65: 18.016 distance: 64 - 66: 39.616 distance: 67 - 68: 46.822 distance: 68 - 69: 48.037 distance: 68 - 71: 23.143 distance: 69 - 70: 35.347 distance: 69 - 78: 15.975 distance: 71 - 72: 10.908 distance: 72 - 73: 22.152 distance: 73 - 74: 12.542 distance: 74 - 75: 15.523 distance: 75 - 76: 10.912 distance: 75 - 77: 16.622 distance: 78 - 79: 20.704 distance: 79 - 80: 18.512 distance: 79 - 82: 40.803 distance: 80 - 81: 21.676 distance: 80 - 86: 44.539 distance: 82 - 83: 30.973 distance: 83 - 84: 27.700 distance: 83 - 85: 55.208 distance: 86 - 87: 19.340 distance: 87 - 88: 42.769 distance: 87 - 90: 44.054 distance: 88 - 89: 54.520 distance: 88 - 94: 37.920 distance: 90 - 91: 22.612 distance: 91 - 92: 22.866 distance: 91 - 93: 10.810 distance: 94 - 95: 18.026 distance: 95 - 96: 22.720 distance: 95 - 98: 22.211 distance: 98 - 99: 30.719 distance: 99 - 100: 45.836 distance: 99 - 101: 29.576 distance: 102 - 103: 5.885 distance: 103 - 104: 59.263 distance: 103 - 106: 34.887 distance: 104 - 105: 25.015 distance: 104 - 109: 25.110 distance: 105 - 130: 38.612 distance: 107 - 108: 40.764 distance: 109 - 110: 41.614 distance: 110 - 111: 16.967 distance: 111 - 112: 23.906 distance: 111 - 113: 32.592 distance: 112 - 135: 32.464 distance: 113 - 114: 44.490 distance: 114 - 115: 47.724 distance: 114 - 117: 24.939 distance: 115 - 116: 24.452 distance: 115 - 122: 27.818 distance: 116 - 144: 28.073 distance: 117 - 118: 46.883 distance: 118 - 119: 14.871 distance: 119 - 120: 18.698 distance: 119 - 121: 15.327 distance: 122 - 123: 25.014 distance: 123 - 124: 43.464 distance: 123 - 126: 20.418 distance: 124 - 125: 40.179 distance: 124 - 130: 56.162 distance: 125 - 153: 35.597 distance: 126 - 127: 35.688 distance: 127 - 128: 16.630 distance: 127 - 129: 12.728 distance: 130 - 131: 17.179 distance: 131 - 132: 31.757 distance: 131 - 134: 40.643 distance: 132 - 133: 10.183 distance: 132 - 135: 25.936 distance: 133 - 158: 30.465 distance: 138 - 164: 3.008