Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 14:06:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/04_2023/7a69_11667_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8175 2.51 5 N 2090 2.21 5 O 2322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 798": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A GLU 1223": "OE1" <-> "OE2" Residue "A ARG 1233": "NH1" <-> "NH2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12637 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 284 Unusual residues: {'CLR': 8, 'R1Q': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 6.90, per 1000 atoms: 0.55 Number of scatterers: 12637 At special positions: 0 Unit cell: (102.48, 208.32, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2322 8.00 N 2090 7.00 C 8175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 95 " distance=2.05 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 200 " distance=2.04 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: 4.93 Conformation dependent library (CDL) restraints added in 1.8 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 15 sheets defined 46.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 45 through 80 removed outlier: 3.550A pdb=" N VAL A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.752A pdb=" N ASP A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 156 Processing helix chain 'A' and resid 162 through 165 No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 168 through 186 removed outlier: 3.957A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.754A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 241 through 259 removed outlier: 4.949A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 270 through 323 removed outlier: 3.666A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 370 removed outlier: 3.826A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 3.528A pdb=" N GLU A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 484 through 491 removed outlier: 4.622A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 533 through 547 removed outlier: 4.377A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 700 through 704 removed outlier: 4.008A pdb=" N ASN A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 704' Processing helix chain 'A' and resid 708 through 738 removed outlier: 4.583A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix Processing helix chain 'A' and resid 745 through 798 Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 812 through 853 removed outlier: 4.526A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 863 removed outlier: 3.794A pdb=" N ALA A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 880 Processing helix chain 'A' and resid 887 through 902 removed outlier: 4.473A pdb=" N ILE A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 removed outlier: 4.032A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 965 removed outlier: 4.194A pdb=" N MET A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.804A pdb=" N ILE A 940 " --> pdb=" O HIS A 936 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET A 949 " --> pdb=" O THR A 945 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 981 Processing helix chain 'A' and resid 986 through 994 Processing helix chain 'A' and resid 999 through 1013 Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1106 through 1112 removed outlier: 3.749A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 removed outlier: 3.934A pdb=" N TYR A1133 " --> pdb=" O GLU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1171 through 1173 No H-bonds generated for 'chain 'A' and resid 1171 through 1173' Processing helix chain 'A' and resid 1178 through 1192 removed outlier: 3.579A pdb=" N VAL A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1222 removed outlier: 3.823A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1238 removed outlier: 3.890A pdb=" N GLN A1238 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 190 through 193 No H-bonds generated for 'chain 'C' and resid 190 through 193' Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing sheet with id= A, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.897A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 608 removed outlier: 6.494A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A 582 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU A 425 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL A 584 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1058 through 1060 Processing sheet with id= D, first strand: chain 'A' and resid 1250 through 1256 removed outlier: 7.084A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS A1254 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A1243 " --> pdb=" O HIS A1254 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A1114 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ASP A1200 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A1116 " --> pdb=" O ASP A1200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.264A pdb=" N LYS B 108 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL B 13 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU B 110 " --> pdb=" O VAL B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 18 through 22 Processing sheet with id= G, first strand: chain 'B' and resid 89 through 95 Processing sheet with id= H, first strand: chain 'B' and resid 119 through 123 Processing sheet with id= I, first strand: chain 'B' and resid 153 through 155 removed outlier: 4.343A pdb=" N TRP B 153 " --> pdb=" O GLN B 161 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 196 through 201 Processing sheet with id= K, first strand: chain 'C' and resid 2 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 112 through 114 removed outlier: 5.781A pdb=" N ARG C 37 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP C 46 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.513A pdb=" N LEU C 129 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR C 180 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C 183 " --> pdb=" O PHE C 171 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.369A pdb=" N ILE C 198 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 174 through 176 642 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2018 1.31 - 1.44: 3412 1.44 - 1.57: 7369 1.57 - 1.70: 33 1.70 - 1.83: 83 Bond restraints: 12915 Sorted by residual: bond pdb=" C50 R1Q A1400 " pdb=" C51 R1Q A1400 " ideal model delta sigma weight residual 1.116 1.604 -0.488 2.00e-02 2.50e+03 5.94e+02 bond pdb=" C53 R1Q A1400 " pdb=" N49 R1Q A1400 " ideal model delta sigma weight residual 1.020 1.419 -0.399 2.00e-02 2.50e+03 3.98e+02 bond pdb=" C43 R1Q A1400 " pdb=" C53 R1Q A1400 " ideal model delta sigma weight residual 1.220 1.525 -0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C48 R1Q A1400 " pdb=" N49 R1Q A1400 " ideal model delta sigma weight residual 1.629 1.324 0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C47 R1Q A1400 " pdb=" C48 R1Q A1400 " ideal model delta sigma weight residual 1.252 1.548 -0.296 2.00e-02 2.50e+03 2.19e+02 ... (remaining 12910 not shown) Histogram of bond angle deviations from ideal: 81.65 - 92.86: 1 92.86 - 104.08: 193 104.08 - 115.29: 8179 115.29 - 126.50: 9023 126.50 - 137.72: 152 Bond angle restraints: 17548 Sorted by residual: angle pdb=" C24 R1Q A1400 " pdb=" C25 R1Q A1400 " pdb=" O26 R1Q A1400 " ideal model delta sigma weight residual 87.19 119.62 -32.43 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C20 R1Q A1400 " pdb=" C25 R1Q A1400 " pdb=" O26 R1Q A1400 " ideal model delta sigma weight residual 150.43 120.27 30.16 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C15 R1Q A1400 " pdb=" C07 R1Q A1400 " pdb=" N08 R1Q A1400 " ideal model delta sigma weight residual 103.15 130.70 -27.55 3.00e+00 1.11e-01 8.43e+01 angle pdb=" C05 R1Q A1400 " pdb=" C06 R1Q A1400 " pdb=" C07 R1Q A1400 " ideal model delta sigma weight residual 111.01 137.72 -26.71 3.00e+00 1.11e-01 7.93e+01 angle pdb=" N TYR B 54 " pdb=" CA TYR B 54 " pdb=" C TYR B 54 " ideal model delta sigma weight residual 113.15 119.98 -6.83 1.19e+00 7.06e-01 3.30e+01 ... (remaining 17543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 6770 16.60 - 33.20: 603 33.20 - 49.80: 163 49.80 - 66.40: 45 66.40 - 83.00: 8 Dihedral angle restraints: 7589 sinusoidal: 3003 harmonic: 4586 Sorted by residual: dihedral pdb=" CA ASN B 216 " pdb=" C ASN B 216 " pdb=" N ARG B 217 " pdb=" CA ARG B 217 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ALA B 99 " pdb=" C ALA B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 7586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.105: 2028 1.105 - 2.209: 1 2.209 - 3.314: 0 3.314 - 4.419: 0 4.419 - 5.523: 2 Chirality restraints: 2031 Sorted by residual: chirality pdb=" C15 R1Q A1400 " pdb=" C07 R1Q A1400 " pdb=" C20 R1Q A1400 " pdb=" C54 R1Q A1400 " both_signs ideal model delta sigma weight residual False 2.79 -2.73 5.52 2.00e-01 2.50e+01 7.63e+02 chirality pdb=" C32 R1Q A1400 " pdb=" C31 R1Q A1400 " pdb=" C34 R1Q A1400 " pdb=" C38 R1Q A1400 " both_signs ideal model delta sigma weight residual False 2.42 -2.76 5.19 2.00e-01 2.50e+01 6.73e+02 chirality pdb=" C53 R1Q A1400 " pdb=" C43 R1Q A1400 " pdb=" C52 R1Q A1400 " pdb=" N49 R1Q A1400 " both_signs ideal model delta sigma weight residual False -1.34 -2.48 1.13 2.00e-01 2.50e+01 3.22e+01 ... (remaining 2028 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 744 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO A 745 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 39 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO C 40 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.020 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE B 94 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.007 2.00e-02 2.50e+03 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 138 2.61 - 3.19: 11358 3.19 - 3.76: 18870 3.76 - 4.33: 26071 4.33 - 4.90: 43663 Nonbonded interactions: 100100 Sorted by model distance: nonbonded pdb=" OD1 ASP A 47 " pdb=" NH1 ARG A 142 " model vdw 2.042 2.520 nonbonded pdb=" NE1 TRP A 803 " pdb=" NZ LYS A1014 " model vdw 2.073 3.200 nonbonded pdb=" CD1 ILE B 53 " pdb=" O ASN B 58 " model vdw 2.128 3.460 nonbonded pdb=" O TYR A 490 " pdb=" NE2 GLN A 912 " model vdw 2.131 2.520 nonbonded pdb=" O GLY A 269 " pdb=" OH TYR A1133 " model vdw 2.171 2.440 ... (remaining 100095 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.210 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: 13.900 Check model and map are aligned: 0.260 Set scattering table: 0.110 Process input model: 34.330 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.014 0.488 12915 Z= 0.864 Angle : 1.060 32.425 17548 Z= 0.506 Chirality : 0.181 5.523 2031 Planarity : 0.004 0.064 2162 Dihedral : 14.343 83.000 4634 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.20 % Rotamer Outliers : 4.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.18), residues: 1584 helix: -1.46 (0.16), residues: 751 sheet: -1.19 (0.28), residues: 295 loop : -2.66 (0.22), residues: 538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 166 time to evaluate : 1.308 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 33 residues processed: 223 average time/residue: 0.2730 time to fit residues: 86.8147 Evaluate side-chains 142 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1483 time to fit residues: 10.3475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 398 HIS A 438 GLN A 537 GLN A 750 GLN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN A1054 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN B 58 ASN B 129 GLN B 143 ASN C 56 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12915 Z= 0.186 Angle : 0.773 25.024 17548 Z= 0.336 Chirality : 0.084 2.318 2031 Planarity : 0.004 0.038 2162 Dihedral : 6.102 98.538 1798 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1584 helix: 0.56 (0.18), residues: 764 sheet: -0.48 (0.29), residues: 286 loop : -2.06 (0.24), residues: 534 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.388 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 146 average time/residue: 0.2443 time to fit residues: 53.8913 Evaluate side-chains 112 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1248 time to fit residues: 5.6700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 0.0020 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN A1130 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN C 196 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12915 Z= 0.260 Angle : 0.777 24.329 17548 Z= 0.341 Chirality : 0.085 2.343 2031 Planarity : 0.003 0.034 2162 Dihedral : 5.977 99.523 1798 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1584 helix: 0.95 (0.19), residues: 774 sheet: -0.18 (0.31), residues: 281 loop : -1.84 (0.24), residues: 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.501 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 0.2633 time to fit residues: 51.2047 Evaluate side-chains 105 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1211 time to fit residues: 5.3065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 71.9424 > 50: distance: 57 - 63: 34.265 distance: 63 - 64: 40.342 distance: 63 - 181: 34.276 distance: 64 - 65: 41.675 distance: 65 - 66: 48.125 distance: 65 - 67: 15.802 distance: 67 - 68: 41.130 distance: 68 - 69: 44.147 distance: 68 - 71: 57.968 distance: 69 - 70: 43.177 distance: 69 - 79: 21.816 distance: 71 - 72: 63.845 distance: 72 - 73: 40.548 distance: 72 - 74: 57.109 distance: 73 - 75: 46.833 distance: 74 - 76: 40.727 distance: 75 - 77: 61.848 distance: 76 - 77: 40.885 distance: 79 - 80: 40.685 distance: 81 - 82: 39.158 distance: 84 - 86: 12.910 distance: 85 - 87: 41.142 distance: 86 - 88: 48.526 distance: 87 - 89: 56.093 distance: 88 - 89: 39.180 distance: 90 - 91: 40.481 distance: 91 - 92: 56.485 distance: 91 - 94: 58.036 distance: 92 - 93: 56.507 distance: 92 - 97: 39.202 distance: 94 - 95: 57.165 distance: 95 - 96: 39.069 distance: 99 - 106: 57.202 distance: 101 - 102: 40.298 distance: 102 - 103: 56.178 distance: 106 - 107: 56.466 distance: 107 - 108: 40.140 distance: 107 - 110: 41.220 distance: 108 - 109: 40.593 distance: 108 - 113: 38.820 distance: 111 - 112: 39.783 distance: 113 - 114: 40.176 distance: 115 - 116: 57.129 distance: 115 - 120: 53.519 distance: 117 - 118: 38.782 distance: 120 - 121: 49.148 distance: 120 - 228: 33.058 distance: 121 - 122: 35.715 distance: 121 - 124: 35.238 distance: 122 - 127: 55.864 distance: 123 - 225: 35.823 distance: 124 - 125: 40.611 distance: 128 - 129: 39.507 distance: 129 - 130: 40.555 distance: 129 - 135: 38.837 distance: 131 - 132: 40.610 distance: 132 - 133: 57.437 distance: 135 - 136: 25.946 distance: 135 - 214: 32.935 distance: 136 - 137: 25.795 distance: 136 - 139: 43.293 distance: 137 - 142: 35.443 distance: 138 - 211: 34.020 distance: 139 - 140: 41.260