Starting phenix.real_space_refine on Mon Dec 11 19:05:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/12_2023/7naf_24271_updated.pdb" } resolution = 3.13 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 378 5.49 5 S 52 5.16 5 C 10433 2.51 5 N 3452 2.21 5 O 4553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 97": "OD1" <-> "OD2" Residue "u PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 98": "OE1" <-> "OE2" Residue "w TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "c TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 76": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 124": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18868 Number of models: 1 Model: "" Number of chains: 17 Chain: "1" Number of atoms: 8046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 8046 Classifications: {'RNA': 378} Modifications used: {'rna2p': 1, 'rna2p_pur': 36, 'rna2p_pyr': 26, 'rna3p': 2, 'rna3p_pur': 154, 'rna3p_pyr': 158} Link IDs: {'rna2p': 63, 'rna3p': 314} Chain breaks: 23 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Chain: "5" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 918 Classifications: {'peptide': 105} Link IDs: {'TRANS': 104} Chain breaks: 2 Chain: "8" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 332 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "u" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 543 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "w" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2959 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 346} Chain breaks: 1 Chain: "b" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 613 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 2 Chain: "d" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 369 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Chain: "U" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 165 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "R" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 529 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain breaks: 2 Chain: "c" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 310 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 2 Chain: "B" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1493 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Chain: "z" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "s" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 66 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "y" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1250 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 8 Chain: "q" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain breaks: 1 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Classifications: {'peptide': 1, 'water': 2} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N SER w 29 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER w 29 " occ=0.50 residue: pdb=" N LEU w 138 " occ=0.50 ... (6 atoms not shown) pdb=" CD2 LEU w 138 " occ=0.50 Time building chain proxies: 10.93, per 1000 atoms: 0.58 Number of scatterers: 18868 At special positions: 0 Unit cell: (142.56, 153.36, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 378 15.00 O 4553 8.00 N 3452 7.00 C 10433 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: 9.61 Conformation dependent library (CDL) restraints added in 2.0 seconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 14 sheets defined 33.5% alpha, 10.1% beta 80 base pairs and 163 stacking pairs defined. Time for finding SS restraints: 9.41 Creating SS restraints... Processing helix chain '5' and resid 33 through 41 Processing helix chain '5' and resid 45 through 93 removed outlier: 3.891A pdb=" N ASN 5 93 " --> pdb=" O LYS 5 89 " (cutoff:3.500A) Processing helix chain '5' and resid 218 through 230 Processing helix chain '8' and resid 6 through 14 removed outlier: 3.511A pdb=" N SER 8 13 " --> pdb=" O LYS 8 9 " (cutoff:3.500A) Processing helix chain '8' and resid 16 through 33 Processing helix chain 'V' and resid 122 through 125 No H-bonds generated for 'chain 'V' and resid 122 through 125' Processing helix chain 'V' and resid 127 through 132 Processing helix chain 'u' and resid 34 through 41 Processing helix chain 'u' and resid 53 through 57 Processing helix chain 'w' and resid 6 through 8 No H-bonds generated for 'chain 'w' and resid 6 through 8' Processing helix chain 'w' and resid 15 through 23 Processing helix chain 'w' and resid 28 through 39 removed outlier: 3.857A pdb=" N ILE w 33 " --> pdb=" O SER w 30 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE w 36 " --> pdb=" O ILE w 33 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN w 37 " --> pdb=" O ILE w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 59 through 67 Processing helix chain 'w' and resid 98 through 107 Processing helix chain 'w' and resid 129 through 147 removed outlier: 4.085A pdb=" N PHE w 133 " --> pdb=" O VAL w 129 " (cutoff:3.500A) Processing helix chain 'w' and resid 167 through 174 Processing helix chain 'w' and resid 210 through 213 Processing helix chain 'w' and resid 215 through 218 No H-bonds generated for 'chain 'w' and resid 215 through 218' Processing helix chain 'w' and resid 230 through 233 No H-bonds generated for 'chain 'w' and resid 230 through 233' Processing helix chain 'w' and resid 259 through 264 Processing helix chain 'w' and resid 268 through 272 Processing helix chain 'w' and resid 285 through 291 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 312 through 328 removed outlier: 3.689A pdb=" N MET w 317 " --> pdb=" O LYS w 313 " (cutoff:3.500A) Processing helix chain 'w' and resid 359 through 386 removed outlier: 3.663A pdb=" N GLN w 386 " --> pdb=" O LEU w 382 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 27 Processing helix chain 'b' and resid 39 through 55 Processing helix chain 'b' and resid 497 through 510 Processing helix chain 'd' and resid 16 through 19 No H-bonds generated for 'chain 'd' and resid 16 through 19' Processing helix chain 'd' and resid 25 through 35 removed outlier: 5.554A pdb=" N ALA d 29 " --> pdb=" O LYS d 26 " (cutoff:3.500A) Proline residue: d 30 - end of helix Processing helix chain 'd' and resid 55 through 60 Processing helix chain 'U' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 109 Processing helix chain 'R' and resid 117 through 128 removed outlier: 3.651A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 144 Processing helix chain 'c' and resid 50 through 53 No H-bonds generated for 'chain 'c' and resid 50 through 53' Processing helix chain 'c' and resid 74 through 81 Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'y' and resid 13 through 16 No H-bonds generated for 'chain 'y' and resid 13 through 16' Processing helix chain 'y' and resid 33 through 37 Processing helix chain 'y' and resid 78 through 83 Processing helix chain 'y' and resid 104 through 107 No H-bonds generated for 'chain 'y' and resid 104 through 107' Processing helix chain 'y' and resid 123 through 126 No H-bonds generated for 'chain 'y' and resid 123 through 126' Processing helix chain 'y' and resid 148 through 151 No H-bonds generated for 'chain 'y' and resid 148 through 151' Processing helix chain 'y' and resid 212 through 217 Processing helix chain 'q' and resid 286 through 292 Processing sheet with id= A, first strand: chain 'V' and resid 22 through 24 removed outlier: 6.644A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'V' and resid 85 through 87 Processing sheet with id= C, first strand: chain 'u' and resid 20 through 22 Processing sheet with id= D, first strand: chain 'w' and resid 89 through 92 removed outlier: 6.680A pdb=" N THR w 115 " --> pdb=" O ILE w 51 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU w 53 " --> pdb=" O THR w 115 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU w 117 " --> pdb=" O LEU w 53 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR w 155 " --> pdb=" O VAL w 116 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N HIS w 118 " --> pdb=" O THR w 155 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL w 157 " --> pdb=" O HIS w 118 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'w' and resid 256 through 258 removed outlier: 6.517A pdb=" N LYS w 277 " --> pdb=" O THR w 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 321 through 325 removed outlier: 5.403A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 55 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 213 through 215 removed outlier: 4.194A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 337 through 339 Processing sheet with id= I, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.586A pdb=" N GLY B 225 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'y' and resid 2 through 4 removed outlier: 6.106A pdb=" N ALA y 204 " --> pdb=" O THR y 3 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'y' and resid 25 through 27 removed outlier: 5.569A pdb=" N VAL y 49 " --> pdb=" O VAL y 26 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'y' and resid 71 through 73 removed outlier: 5.877A pdb=" N GLN y 95 " --> pdb=" O VAL y 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'y' and resid 108 through 110 removed outlier: 6.304A pdb=" N GLU y 136 " --> pdb=" O ALA y 115 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL y 117 " --> pdb=" O GLU y 136 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE y 138 " --> pdb=" O VAL y 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'q' and resid 294 through 297 removed outlier: 3.591A pdb=" N ASP q 311 " --> pdb=" O ASN q 295 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN q 297 " --> pdb=" O ILE q 309 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE q 309 " --> pdb=" O GLN q 297 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 200 hydrogen bonds 330 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 163 stacking parallelities Total time for adding SS restraints: 7.65 Time building geometry restraints manager: 10.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3874 1.33 - 1.46: 6755 1.46 - 1.58: 8491 1.58 - 1.70: 731 1.70 - 1.83: 87 Bond restraints: 19938 Sorted by residual: bond pdb=" C2' A2M 12946 " pdb=" C1' A2M 12946 " ideal model delta sigma weight residual 1.305 1.555 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" O4' A2M 12946 " pdb=" C1' A2M 12946 " ideal model delta sigma weight residual 1.615 1.412 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" P A2M 12946 " pdb=" O5' A2M 12946 " ideal model delta sigma weight residual 1.647 1.828 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" C5 OMU 12921 " pdb=" C6 OMU 12921 " ideal model delta sigma weight residual 1.480 1.355 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C4' A2M 12946 " pdb=" O4' A2M 12946 " ideal model delta sigma weight residual 1.305 1.429 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 19933 not shown) Histogram of bond angle deviations from ideal: 90.60 - 99.28: 3 99.28 - 107.96: 3406 107.96 - 116.64: 13024 116.64 - 125.32: 10660 125.32 - 134.00: 1462 Bond angle restraints: 28555 Sorted by residual: angle pdb=" C1' A2M 12946 " pdb=" N9 A2M 12946 " pdb=" C8 A2M 12946 " ideal model delta sigma weight residual 88.50 128.04 -39.54 3.00e+00 1.11e-01 1.74e+02 angle pdb=" N6 A2M 12946 " pdb=" C6 A2M 12946 " pdb=" N1 A2M 12946 " ideal model delta sigma weight residual 92.14 118.65 -26.51 3.00e+00 1.11e-01 7.81e+01 angle pdb=" C1' OMG 12922 " pdb=" N9 OMG 12922 " pdb=" C4 OMG 12922 " ideal model delta sigma weight residual 108.29 126.65 -18.36 3.00e+00 1.11e-01 3.75e+01 angle pdb=" C1' OMG 12922 " pdb=" N9 OMG 12922 " pdb=" C8 OMG 12922 " ideal model delta sigma weight residual 142.82 126.64 16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" N1 A2M 12946 " pdb=" C2 A2M 12946 " pdb=" N3 A2M 12946 " ideal model delta sigma weight residual 120.08 131.42 -11.34 3.00e+00 1.11e-01 1.43e+01 ... (remaining 28550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 11277 35.25 - 70.50: 745 70.50 - 105.75: 124 105.75 - 141.00: 2 141.00 - 176.25: 9 Dihedral angle restraints: 12157 sinusoidal: 8320 harmonic: 3837 Sorted by residual: dihedral pdb=" O4' U 13019 " pdb=" C1' U 13019 " pdb=" N1 U 13019 " pdb=" C2 U 13019 " ideal model delta sinusoidal sigma weight residual 200.00 29.91 170.09 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U 12829 " pdb=" C1' U 12829 " pdb=" N1 U 12829 " pdb=" C2 U 12829 " ideal model delta sinusoidal sigma weight residual 200.00 53.89 146.11 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' C 12825 " pdb=" C1' C 12825 " pdb=" N1 C 12825 " pdb=" C2 C 12825 " ideal model delta sinusoidal sigma weight residual 232.00 55.94 176.06 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3254 0.061 - 0.123: 224 0.123 - 0.184: 15 0.184 - 0.245: 5 0.245 - 0.307: 1 Chirality restraints: 3499 Sorted by residual: chirality pdb=" C2' A2M 12946 " pdb=" C3' A2M 12946 " pdb=" O2' A2M 12946 " pdb=" C1' A2M 12946 " both_signs ideal model delta sigma weight residual False -2.39 -2.70 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1' A2M 12946 " pdb=" O4' A2M 12946 " pdb=" C2' A2M 12946 " pdb=" N9 A2M 12946 " both_signs ideal model delta sigma weight residual False 2.40 2.62 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C4' A2M 12946 " pdb=" C5' A2M 12946 " pdb=" O4' A2M 12946 " pdb=" C3' A2M 12946 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 3496 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12922 " -0.032 2.00e-02 2.50e+03 4.89e-01 5.37e+03 pdb=" C4' OMG 12922 " -0.401 2.00e-02 2.50e+03 pdb=" O4' OMG 12922 " -0.438 2.00e-02 2.50e+03 pdb=" C3' OMG 12922 " 0.577 2.00e-02 2.50e+03 pdb=" O3' OMG 12922 " 0.446 2.00e-02 2.50e+03 pdb=" C2' OMG 12922 " 0.248 2.00e-02 2.50e+03 pdb=" O2' OMG 12922 " -0.824 2.00e-02 2.50e+03 pdb=" C1' OMG 12922 " -0.252 2.00e-02 2.50e+03 pdb=" N9 OMG 12922 " 0.677 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 11857 " 0.024 2.00e-02 2.50e+03 1.32e-02 3.90e+00 pdb=" N1 C 11857 " -0.031 2.00e-02 2.50e+03 pdb=" C2 C 11857 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C 11857 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C 11857 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C 11857 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C 11857 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C 11857 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C 11857 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11303 " -0.026 2.00e-02 2.50e+03 1.16e-02 3.70e+00 pdb=" N9 A 11303 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A 11303 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 11303 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 11303 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 11303 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 11303 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 11303 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 11303 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 11303 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 11303 " 0.003 2.00e-02 2.50e+03 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1290 2.72 - 3.26: 17270 3.26 - 3.81: 33304 3.81 - 4.35: 42130 4.35 - 4.90: 62399 Nonbonded interactions: 156393 Sorted by model distance: nonbonded pdb=" O2' G 11789 " pdb=" O5' G 11790 " model vdw 2.172 2.440 nonbonded pdb=" O2' C 12343 " pdb=" OP1 U 13056 " model vdw 2.192 2.440 nonbonded pdb=" O2' G 11899 " pdb=" O4 U 12334 " model vdw 2.215 2.440 nonbonded pdb=" O2 C 13060 " pdb=" O2' U 13332 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR B 54 " pdb=" O ASP B 360 " model vdw 2.226 2.440 ... (remaining 156388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.330 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 59.470 Find NCS groups from input model: 0.450 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.005 0.250 19938 Z= 0.273 Angle : 0.622 39.539 28555 Z= 0.279 Chirality : 0.034 0.307 3499 Planarity : 0.011 0.489 2222 Dihedral : 20.384 176.246 9657 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1261 helix: 1.71 (0.24), residues: 479 sheet: -0.01 (0.45), residues: 146 loop : -0.76 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP u 51 HIS 0.004 0.001 HIS y 162 PHE 0.009 0.001 PHE b 45 TYR 0.013 0.001 TYR c 27 ARG 0.004 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.488 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3696 time to fit residues: 101.7511 Evaluate side-chains 149 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 224 ASN w 235 ASN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19938 Z= 0.210 Angle : 0.564 17.411 28555 Z= 0.291 Chirality : 0.035 0.218 3499 Planarity : 0.004 0.124 2222 Dihedral : 21.232 175.854 6838 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.86 % Allowed : 7.38 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.33 (0.24), residues: 1261 helix: 1.61 (0.24), residues: 483 sheet: -0.18 (0.45), residues: 148 loop : -0.77 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP u 51 HIS 0.004 0.001 HIS y 162 PHE 0.016 0.001 PHE 5 88 TYR 0.013 0.001 TYR R 124 ARG 0.004 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 1.693 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 158 average time/residue: 0.3470 time to fit residues: 82.4592 Evaluate side-chains 153 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1664 time to fit residues: 4.1927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19938 Z= 0.310 Angle : 0.634 16.332 28555 Z= 0.326 Chirality : 0.038 0.239 3499 Planarity : 0.005 0.127 2222 Dihedral : 21.277 175.352 6838 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.03 % Allowed : 10.63 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.06 (0.23), residues: 1261 helix: 1.28 (0.24), residues: 482 sheet: -0.20 (0.43), residues: 148 loop : -0.87 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP u 51 HIS 0.007 0.002 HIS y 50 PHE 0.027 0.002 PHE 5 88 TYR 0.016 0.002 TYR w 17 ARG 0.005 0.001 ARG w 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 1.569 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 159 average time/residue: 0.3433 time to fit residues: 81.2420 Evaluate side-chains 144 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1768 time to fit residues: 3.5549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 130 ASN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19938 Z= 0.236 Angle : 0.585 16.022 28555 Z= 0.303 Chirality : 0.036 0.237 3499 Planarity : 0.005 0.124 2222 Dihedral : 21.247 176.207 6838 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.54 % Allowed : 12.52 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.03 (0.23), residues: 1261 helix: 1.22 (0.24), residues: 484 sheet: -0.07 (0.43), residues: 144 loop : -0.90 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP w 287 HIS 0.006 0.001 HIS y 50 PHE 0.011 0.001 PHE V 11 TYR 0.014 0.001 TYR w 17 ARG 0.004 0.000 ARG w 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.509 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 164 average time/residue: 0.3395 time to fit residues: 83.3547 Evaluate side-chains 148 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1785 time to fit residues: 4.6711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19938 Z= 0.155 Angle : 0.543 16.040 28555 Z= 0.281 Chirality : 0.034 0.225 3499 Planarity : 0.004 0.121 2222 Dihedral : 21.152 176.834 6838 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.11 % Allowed : 13.81 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.16 (0.24), residues: 1261 helix: 1.42 (0.24), residues: 483 sheet: -0.08 (0.46), residues: 140 loop : -0.88 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP w 287 HIS 0.003 0.001 HIS y 162 PHE 0.009 0.001 PHE w 91 TYR 0.016 0.001 TYR y 35 ARG 0.003 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.547 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 161 average time/residue: 0.3340 time to fit residues: 80.1661 Evaluate side-chains 155 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1741 time to fit residues: 4.5229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 72.0396 > 50: distance: 50 - 66: 26.968 distance: 54 - 74: 37.789 distance: 58 - 83: 34.285 distance: 61 - 66: 28.271 distance: 62 - 88: 32.972 distance: 66 - 67: 45.728 distance: 67 - 70: 40.941 distance: 68 - 69: 24.562 distance: 68 - 74: 39.945 distance: 69 - 96: 50.440 distance: 71 - 72: 38.368 distance: 71 - 73: 40.263 distance: 74 - 75: 40.594 distance: 75 - 76: 28.981 distance: 75 - 78: 49.719 distance: 76 - 77: 64.310 distance: 76 - 83: 10.541 distance: 77 - 105: 41.702 distance: 78 - 79: 10.569 distance: 79 - 80: 56.190 distance: 80 - 81: 57.143 distance: 80 - 82: 39.190 distance: 83 - 84: 9.934 distance: 84 - 85: 63.596 distance: 84 - 87: 8.919 distance: 85 - 86: 67.926 distance: 85 - 88: 39.257 distance: 86 - 113: 57.879 distance: 88 - 89: 40.280 distance: 89 - 92: 15.757 distance: 90 - 91: 39.797 distance: 90 - 96: 41.033 distance: 91 - 118: 55.568 distance: 92 - 93: 40.576 distance: 93 - 94: 41.011 distance: 93 - 95: 45.003 distance: 96 - 97: 39.239 distance: 97 - 98: 40.309 distance: 98 - 99: 39.618 distance: 98 - 105: 57.446 distance: 100 - 101: 25.427 distance: 101 - 102: 35.409 distance: 102 - 103: 10.551 distance: 103 - 104: 57.016 distance: 106 - 107: 56.794 distance: 106 - 109: 41.127 distance: 107 - 113: 6.262 distance: 110 - 111: 4.909 distance: 110 - 112: 40.880 distance: 113 - 114: 6.747 distance: 114 - 115: 8.177 distance: 114 - 117: 39.727 distance: 115 - 116: 33.672 distance: 115 - 118: 5.985 distance: 118 - 119: 56.416 distance: 120 - 121: 40.979 distance: 120 - 125: 4.130 distance: 122 - 124: 40.389 distance: 125 - 126: 36.323 distance: 126 - 129: 38.511 distance: 127 - 128: 39.906 distance: 129 - 130: 40.719 distance: 130 - 131: 38.534 distance: 131 - 132: 28.489 distance: 134 - 135: 40.860 distance: 135 - 138: 37.554 distance: 136 - 137: 29.227 distance: 136 - 142: 32.700 distance: 138 - 139: 14.350 distance: 139 - 140: 19.490 distance: 139 - 141: 45.150