Starting phenix.real_space_refine on Tue Jul 23 02:40:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/07_2024/7v00_26924_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/07_2024/7v00_26924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/07_2024/7v00_26924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/07_2024/7v00_26924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/07_2024/7v00_26924_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/07_2024/7v00_26924_neut.cif" } resolution = 3.87 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= -0.001 sd= 0.030 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 36 5.49 5 S 56 5.16 5 C 12877 2.51 5 N 3440 2.21 5 O 4011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "F GLU 521": "OE1" <-> "OE2" Residue "F GLU 610": "OE1" <-> "OE2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "H TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20420 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2473 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 3 Chain: "F" Number of atoms: 5652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5652 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 7, 'TRANS': 687} Chain breaks: 3 Chain: "G" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 637 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 871 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.22, per 1000 atoms: 0.60 Number of scatterers: 20420 At special positions: 0 Unit cell: (93.003, 120.797, 209.524, 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 56 16.00 P 36 15.00 O 4011 8.00 N 3440 7.00 C 12877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.07 Conformation dependent library (CDL) restraints added in 3.6 seconds 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 28 sheets defined 48.4% alpha, 15.7% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 6.77 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.696A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 removed outlier: 3.771A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.685A pdb=" N ASN A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 47 through 62 removed outlier: 3.501A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.564A pdb=" N ASN B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.559A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 4.446A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.764A pdb=" N GLY C 188 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 removed outlier: 3.625A pdb=" N ILE D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 115 removed outlier: 3.587A pdb=" N ASN D 114 " --> pdb=" O HIS D 110 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP D 115 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 75 through 82 removed outlier: 3.687A pdb=" N GLN E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 147 removed outlier: 3.678A pdb=" N ILE E 134 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 156 removed outlier: 4.191A pdb=" N SER E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 211 through 230 Processing helix chain 'E' and resid 237 through 247 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 278 through 293 Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.709A pdb=" N MET E 300 " --> pdb=" O TYR E 297 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 303 " --> pdb=" O MET E 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 16 through 24 removed outlier: 3.872A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.653A pdb=" N LEU F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 67 removed outlier: 4.096A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 116 through 122 removed outlier: 4.490A pdb=" N ILE F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 170 removed outlier: 4.246A pdb=" N TYR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.900A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 273 through 300 removed outlier: 3.596A pdb=" N SER F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.612A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.774A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 437 removed outlier: 4.530A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'F' and resid 500 through 505 removed outlier: 3.885A pdb=" N ASN F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 518 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 550 through 573 removed outlier: 3.625A pdb=" N THR F 554 " --> pdb=" O SER F 550 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU F 569 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN F 570 " --> pdb=" O LYS F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 612 Processing helix chain 'F' and resid 630 through 636 removed outlier: 3.990A pdb=" N PHE F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 674 through 686 Processing helix chain 'F' and resid 690 through 703 removed outlier: 4.005A pdb=" N ASN F 703 " --> pdb=" O ALA F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 719 Processing helix chain 'F' and resid 722 through 734 Processing helix chain 'F' and resid 735 through 750 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.907A pdb=" N GLU I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 44 through 47 Processing helix chain 'J' and resid 48 through 61 Processing helix chain 'J' and resid 75 through 92 removed outlier: 3.646A pdb=" N GLU J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 103 through 115 Processing helix chain 'J' and resid 116 through 137 Processing helix chain 'K' and resid 15 through 24 removed outlier: 5.083A pdb=" N VAL K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER K 23 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 65 Processing helix chain 'K' and resid 71 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 115 Processing helix chain 'K' and resid 116 through 137 removed outlier: 3.889A pdb=" N TYR K 137 " --> pdb=" O TYR K 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 5.574A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 9 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS A 4 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR A 201 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 6 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 199 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 8 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A 197 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 124 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.511A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.471A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.571A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.571A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AA9, first strand: chain 'D' and resid 96 through 103 removed outlier: 5.649A pdb=" N LEU D 96 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN D 155 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE D 98 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE D 153 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP D 100 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL D 151 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 9 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.510A pdb=" N LEU D 43 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 119 through 124 Processing sheet with id=AB3, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.938A pdb=" N GLN E 22 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 38 through 41 Processing sheet with id=AB6, first strand: chain 'E' and resid 184 through 193 removed outlier: 7.185A pdb=" N MET E 186 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP E 178 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU E 188 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN E 175 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR E 315 " --> pdb=" O GLN E 175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 307 through 311 removed outlier: 6.569A pdb=" N TYR F 316 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR F 310 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 315 " --> pdb=" O MET F 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 417 through 418 Processing sheet with id=AB9, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.678A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 461 " --> pdb=" O PHE F 441 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 578 through 584 removed outlier: 7.402A pdb=" N ILE F 578 " --> pdb=" O ALA F 593 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA F 593 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA F 580 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 591 " --> pdb=" O ALA F 580 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL F 528 " --> pdb=" O GLY F 623 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.518A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AC5, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC6, first strand: chain 'H' and resid 273 through 274 Processing sheet with id=AC7, first strand: chain 'H' and resid 243 through 246 removed outlier: 3.693A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC9, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.552A pdb=" N LYS I 26 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL I 38 " --> pdb=" O LYS I 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'J' and resid 25 through 26 939 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 8.79 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: 6038 1.33 - 1.46: 4261 1.46 - 1.58: 10386 1.58 - 1.70: 70 1.70 - 1.82: 99 Bond restraints: 20854 Sorted by residual: bond pdb=" C1' A G 17 " pdb=" N9 A G 17 " ideal model delta sigma weight residual 1.475 1.386 0.089 1.50e-02 4.44e+03 3.50e+01 bond pdb=" C1' U G 19 " pdb=" N1 U G 19 " ideal model delta sigma weight residual 1.480 1.567 -0.087 1.50e-02 4.44e+03 3.33e+01 bond pdb=" C1' C G 28 " pdb=" N1 C G 28 " ideal model delta sigma weight residual 1.480 1.565 -0.085 1.50e-02 4.44e+03 3.19e+01 bond pdb=" C1' A G 16 " pdb=" N9 A G 16 " ideal model delta sigma weight residual 1.475 1.402 0.073 1.50e-02 4.44e+03 2.38e+01 bond pdb=" C1' U G 9 " pdb=" N1 U G 9 " ideal model delta sigma weight residual 1.470 1.540 -0.070 1.50e-02 4.44e+03 2.16e+01 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 95.53 - 103.69: 222 103.69 - 111.85: 9632 111.85 - 120.01: 9202 120.01 - 128.17: 8982 128.17 - 136.33: 143 Bond angle restraints: 28181 Sorted by residual: angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 130.39 9.48 1.00e+00 1.00e+00 8.99e+01 angle pdb=" CA PHE F 540 " pdb=" CB PHE F 540 " pdb=" CG PHE F 540 " ideal model delta sigma weight residual 113.80 107.01 6.79 1.00e+00 1.00e+00 4.61e+01 angle pdb=" C THR F 539 " pdb=" N PHE F 540 " pdb=" CA PHE F 540 " ideal model delta sigma weight residual 120.31 111.85 8.46 1.52e+00 4.33e-01 3.10e+01 angle pdb=" C5' ATP F 801 " pdb=" O5' ATP F 801 " pdb=" PA ATP F 801 " ideal model delta sigma weight residual 121.27 116.99 4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" N MET E 186 " pdb=" CA MET E 186 " pdb=" C MET E 186 " ideal model delta sigma weight residual 110.07 104.81 5.26 1.26e+00 6.30e-01 1.74e+01 ... (remaining 28176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 12230 31.68 - 63.35: 327 63.35 - 95.03: 42 95.03 - 126.70: 4 126.70 - 158.37: 3 Dihedral angle restraints: 12606 sinusoidal: 5528 harmonic: 7078 Sorted by residual: dihedral pdb=" O4' C G 28 " pdb=" C1' C G 28 " pdb=" N1 C G 28 " pdb=" C2 C G 28 " ideal model delta sinusoidal sigma weight residual 200.00 50.60 149.40 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" CB CYS F 410 " pdb=" SG CYS F 410 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual -86.00 -158.23 72.23 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 30.37 -158.37 1 1.70e+01 3.46e-03 6.41e+01 ... (remaining 12603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2509 0.066 - 0.132: 516 0.132 - 0.198: 53 0.198 - 0.264: 8 0.264 - 0.330: 3 Chirality restraints: 3089 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE C 91 " pdb=" CA ILE C 91 " pdb=" CG1 ILE C 91 " pdb=" CG2 ILE C 91 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE D 46 " pdb=" CA ILE D 46 " pdb=" CG1 ILE D 46 " pdb=" CG2 ILE D 46 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3086 not shown) Planarity restraints: 3493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 339 " -0.031 2.00e-02 2.50e+03 3.08e-02 2.38e+01 pdb=" CG TRP F 339 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP F 339 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 339 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 339 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 339 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP F 339 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 129 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C THR F 129 " 0.067 2.00e-02 2.50e+03 pdb=" O THR F 129 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN F 130 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 85 " -0.022 2.00e-02 2.50e+03 2.20e-02 8.49e+00 pdb=" CG PHE I 85 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 85 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE I 85 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE I 85 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 85 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE I 85 " -0.001 2.00e-02 2.50e+03 ... (remaining 3490 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 156 2.57 - 3.15: 17450 3.15 - 3.73: 30144 3.73 - 4.32: 42625 4.32 - 4.90: 69362 Nonbonded interactions: 159737 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.987 2.520 nonbonded pdb=" O TYR H 71 " pdb=" OH TYR H 162 " model vdw 2.035 2.440 nonbonded pdb=" OG1 THR C 126 " pdb=" O2' U G 25 " model vdw 2.056 2.440 nonbonded pdb=" NH1 ARG C 129 " pdb=" OD1 ASN D 57 " model vdw 2.057 2.520 nonbonded pdb=" O LEU E 55 " pdb=" OG1 THR E 58 " model vdw 2.118 2.440 ... (remaining 159732 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' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'B' and resid 2 through 208) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 139)) selection = chain 'J' selection = (chain 'K' and (resid 17 through 61 or resid 74 through 139)) } 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 group one per residue 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: 7.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 60.370 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 0.092 20854 Z= 0.382 Angle : 0.862 10.663 28181 Z= 0.497 Chirality : 0.053 0.330 3089 Planarity : 0.004 0.065 3493 Dihedral : 14.507 158.375 8053 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 0.32 % Allowed : 0.69 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2378 helix: 0.09 (0.15), residues: 1038 sheet: 0.13 (0.26), residues: 387 loop : -1.82 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP F 339 HIS 0.007 0.002 HIS I 18 PHE 0.051 0.003 PHE I 85 TYR 0.030 0.002 TYR F 582 ARG 0.019 0.002 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 444 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 110 HIS cc_start: 0.8270 (t-90) cc_final: 0.7697 (t-170) REVERT: D 131 THR cc_start: 0.8024 (p) cc_final: 0.7390 (p) REVERT: E 28 ASP cc_start: 0.8385 (m-30) cc_final: 0.7785 (m-30) REVERT: E 33 PHE cc_start: 0.8218 (m-10) cc_final: 0.7706 (m-80) REVERT: E 41 ILE cc_start: 0.8233 (mm) cc_final: 0.8017 (mp) REVERT: F 222 ASP cc_start: 0.8014 (m-30) cc_final: 0.7805 (m-30) REVERT: F 624 MET cc_start: 0.7867 (ttm) cc_final: 0.7514 (tpt) REVERT: I 85 PHE cc_start: 0.8837 (m-80) cc_final: 0.8540 (m-80) REVERT: I 104 MET cc_start: 0.8553 (mmm) cc_final: 0.8349 (tmm) REVERT: I 119 PHE cc_start: 0.9040 (t80) cc_final: 0.8747 (t80) REVERT: J 18 HIS cc_start: 0.7377 (t-170) cc_final: 0.6669 (t70) REVERT: J 126 TYR cc_start: 0.8998 (t80) cc_final: 0.8745 (t80) REVERT: K 50 ASN cc_start: 0.8962 (m-40) cc_final: 0.8045 (m110) outliers start: 7 outliers final: 0 residues processed: 449 average time/residue: 0.3906 time to fit residues: 250.5563 Evaluate side-chains 230 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS E 316 ASN E 320 HIS ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN F 474 ASN F 482 ASN F 560 GLN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 ASN ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN I 27 ASN K 24 ASN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20854 Z= 0.456 Angle : 0.829 10.728 28181 Z= 0.441 Chirality : 0.048 0.320 3089 Planarity : 0.005 0.044 3493 Dihedral : 14.047 164.922 3140 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.98 % Allowed : 10.24 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.76 (0.16), residues: 2378 helix: 0.27 (0.15), residues: 1073 sheet: 0.21 (0.26), residues: 390 loop : -1.73 (0.18), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP F 339 HIS 0.011 0.002 HIS D 110 PHE 0.029 0.003 PHE I 85 TYR 0.031 0.002 TYR J 86 ARG 0.012 0.001 ARG D 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 157 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.7036 (mtmm) REVERT: E 186 MET cc_start: 0.8506 (mmm) cc_final: 0.8092 (mpp) REVERT: F 341 MET cc_start: 0.8162 (mmm) cc_final: 0.7862 (mmm) REVERT: F 496 MET cc_start: 0.7167 (pmm) cc_final: 0.6936 (pmm) REVERT: F 540 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8037 (t80) REVERT: F 695 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.4929 (m-80) REVERT: I 54 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8874 (mm-40) REVERT: I 85 PHE cc_start: 0.8975 (m-80) cc_final: 0.8676 (m-80) REVERT: I 86 TYR cc_start: 0.8200 (m-80) cc_final: 0.7779 (m-80) REVERT: I 97 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: I 127 PHE cc_start: 0.9392 (t80) cc_final: 0.9146 (t80) REVERT: J 18 HIS cc_start: 0.7657 (t-170) cc_final: 0.7264 (t70) outliers start: 43 outliers final: 26 residues processed: 245 average time/residue: 0.3523 time to fit residues: 129.2706 Evaluate side-chains 209 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 124 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN C 193 GLN D 110 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN F 14 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 ASN F 549 ASN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 740 ASN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20854 Z= 0.235 Angle : 0.637 9.575 28181 Z= 0.339 Chirality : 0.043 0.242 3089 Planarity : 0.003 0.038 3493 Dihedral : 13.898 165.348 3140 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.94 % Allowed : 11.90 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2378 helix: 0.72 (0.16), residues: 1066 sheet: 0.27 (0.26), residues: 390 loop : -1.55 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 339 HIS 0.008 0.001 HIS F 26 PHE 0.063 0.002 PHE J 85 TYR 0.022 0.002 TYR H 184 ARG 0.006 0.001 ARG K 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 193 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 MET cc_start: 0.8380 (mmm) cc_final: 0.7901 (mpp) REVERT: F 432 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8733 (tp) REVERT: F 452 MET cc_start: 0.7373 (mmm) cc_final: 0.7035 (mmp) REVERT: F 496 MET cc_start: 0.7434 (pmm) cc_final: 0.7116 (pmm) REVERT: F 540 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7978 (t80) REVERT: F 624 MET cc_start: 0.8005 (tpp) cc_final: 0.7666 (tpt) REVERT: F 665 ASP cc_start: 0.8298 (p0) cc_final: 0.8018 (p0) REVERT: F 695 TYR cc_start: 0.6005 (OUTLIER) cc_final: 0.4947 (m-80) REVERT: H 13 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8226 (ptpp) REVERT: J 18 HIS cc_start: 0.7797 (t-170) cc_final: 0.7080 (t70) REVERT: J 137 TYR cc_start: 0.7062 (m-80) cc_final: 0.6819 (m-80) outliers start: 42 outliers final: 25 residues processed: 225 average time/residue: 0.3568 time to fit residues: 120.5810 Evaluate side-chains 203 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain K residue 50 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20854 Z= 0.267 Angle : 0.626 9.705 28181 Z= 0.333 Chirality : 0.042 0.186 3089 Planarity : 0.003 0.036 3493 Dihedral : 13.782 168.197 3140 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.03 % Allowed : 12.55 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2378 helix: 0.78 (0.16), residues: 1080 sheet: 0.29 (0.26), residues: 395 loop : -1.56 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.013 0.001 HIS K 18 PHE 0.019 0.002 PHE F 44 TYR 0.029 0.002 TYR J 126 ARG 0.005 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 128 ASN cc_start: 0.8057 (t0) cc_final: 0.7848 (t0) REVERT: E 186 MET cc_start: 0.8472 (mmm) cc_final: 0.7957 (mpp) REVERT: F 452 MET cc_start: 0.7502 (mmm) cc_final: 0.7190 (mmp) REVERT: F 496 MET cc_start: 0.7521 (pmm) cc_final: 0.7144 (pmm) REVERT: F 540 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.8022 (t80) REVERT: F 624 MET cc_start: 0.8050 (tpp) cc_final: 0.7720 (tpt) REVERT: F 665 ASP cc_start: 0.8387 (p0) cc_final: 0.8059 (p0) REVERT: F 695 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.4912 (m-80) REVERT: H 13 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8082 (ptpp) REVERT: I 77 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8843 (mm-30) REVERT: I 96 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: I 110 ARG cc_start: 0.6607 (ptt180) cc_final: 0.6235 (ptt180) REVERT: I 119 PHE cc_start: 0.8940 (t80) cc_final: 0.8208 (t80) REVERT: J 18 HIS cc_start: 0.7595 (t-170) cc_final: 0.6741 (t-170) REVERT: J 107 ILE cc_start: 0.8330 (mm) cc_final: 0.8054 (mt) REVERT: J 133 TYR cc_start: 0.7269 (m-80) cc_final: 0.6964 (m-80) outliers start: 44 outliers final: 30 residues processed: 217 average time/residue: 0.3587 time to fit residues: 118.7737 Evaluate side-chains 203 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 471 GLN Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 50 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/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-dev-5388/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-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/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-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/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-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.02 > 50: distance: 10 - 16: 31.679 distance: 16 - 17: 5.364 distance: 17 - 18: 23.126 distance: 17 - 20: 40.810 distance: 18 - 19: 40.416 distance: 18 - 22: 26.957 distance: 20 - 21: 30.529 distance: 22 - 23: 17.354 distance: 23 - 24: 17.488 distance: 24 - 25: 14.870 distance: 24 - 26: 11.327 distance: 26 - 27: 6.622 distance: 27 - 28: 12.394 distance: 27 - 30: 10.710 distance: 28 - 29: 31.951 distance: 28 - 32: 11.502 distance: 30 - 31: 22.627 distance: 32 - 33: 9.844 distance: 33 - 34: 5.070 distance: 33 - 36: 23.955 distance: 34 - 35: 15.012 distance: 34 - 41: 6.610 distance: 35 - 63: 18.371 distance: 36 - 37: 22.296 distance: 37 - 38: 10.507 distance: 38 - 39: 3.997 distance: 39 - 40: 5.289 distance: 41 - 42: 4.963 distance: 42 - 43: 7.062 distance: 42 - 45: 7.732 distance: 43 - 44: 6.964 distance: 43 - 46: 9.086 distance: 44 - 69: 20.387 distance: 46 - 47: 6.273 distance: 47 - 48: 9.547 distance: 47 - 50: 4.499 distance: 48 - 49: 11.140 distance: 48 - 54: 10.589 distance: 49 - 77: 8.291 distance: 50 - 51: 4.210 distance: 51 - 53: 3.755 distance: 54 - 55: 5.115 distance: 55 - 56: 3.189 distance: 55 - 58: 5.182 distance: 56 - 57: 13.431 distance: 56 - 63: 6.445 distance: 58 - 59: 9.076 distance: 59 - 60: 8.108 distance: 60 - 61: 8.310 distance: 61 - 62: 3.837 distance: 63 - 64: 8.999 distance: 64 - 65: 5.829 distance: 64 - 67: 6.736 distance: 65 - 66: 7.482 distance: 65 - 69: 20.723 distance: 66 - 94: 11.509 distance: 67 - 68: 13.102 distance: 69 - 70: 8.215 distance: 70 - 71: 8.029 distance: 70 - 73: 6.455 distance: 71 - 72: 15.065 distance: 71 - 77: 10.176 distance: 72 - 101: 20.759 distance: 73 - 74: 7.835 distance: 74 - 75: 11.060 distance: 74 - 76: 6.361 distance: 78 - 81: 3.556 distance: 79 - 80: 3.767 distance: 79 - 88: 4.875 distance: 82 - 83: 12.338 distance: 83 - 84: 3.825