Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 11:44:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/07_2023/7yq6_34021_updated.pdb" } resolution = 4.18 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= 0.003 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 484 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 S 98 5.16 5 C 8722 2.51 5 N 2419 2.21 5 O 2691 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ARG 331": "NH1" <-> "NH2" Residue "E GLU 362": "OE1" <-> "OE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 443": "OE1" <-> "OE2" Residue "E ARG 576": "NH1" <-> "NH2" Residue "E GLU 633": "OE1" <-> "OE2" Residue "E GLU 640": "OE1" <-> "OE2" Residue "E GLU 855": "OE1" <-> "OE2" Residue "E ARG 863": "NH1" <-> "NH2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 517": "OE1" <-> "OE2" Residue "F ARG 576": "NH1" <-> "NH2" Residue "F GLU 637": "OE1" <-> "OE2" Residue "F GLU 808": "OE1" <-> "OE2" Residue "F GLU 824": "OE1" <-> "OE2" Residue "F TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 855": "OE1" <-> "OE2" Residue "F GLU 856": "OE1" <-> "OE2" Residue "F ARG 863": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 13990 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 6439 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 799, 6432 Classifications: {'peptide': 799} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 754} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 799, 6432 Classifications: {'peptide': 799} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 754} Chain breaks: 2 bond proxies already assigned to first conformer: 6583 Chain: "F" Number of atoms: 6397 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 793, 6390 Classifications: {'peptide': 793} Link IDs: {'CIS': 1, 'PTRANS': 42, 'TRANS': 749} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 793, 6390 Classifications: {'peptide': 793} Link IDs: {'CIS': 1, 'PTRANS': 42, 'TRANS': 749} Chain breaks: 2 bond proxies already assigned to first conformer: 6540 Chain: "G" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 577 Classifications: {'DNA': 21, 'RNA': 3} Modifications used: {'rna2p': 1, 'rna3p': 2} Link IDs: {'rna2p': 1, 'rna3p': 22} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 6 Chain: "H" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 577 Classifications: {'DNA': 21, 'RNA': 3} Modifications used: {'rna2p': 1, 'rna3p': 2} Link IDs: {'rna2p': 1, 'rna3p': 22} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 12.08, per 1000 atoms: 0.86 Number of scatterers: 13990 At special positions: 0 Unit cell: (160.5, 92.02, 158.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 48 15.00 F 12 9.00 O 2691 8.00 N 2419 7.00 C 8722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.05 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.04 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.04 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.04 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.04 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.04 Simple disulfide: pdb=" SG CYS E 524 " - pdb=" SG CYS F 524 " distance=2.04 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.04 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.05 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.04 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.04 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.04 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.04 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.37 Conformation dependent library (CDL) restraints added in 3.6 seconds 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3002 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 22 sheets defined 7.4% alpha, 16.9% beta 0 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.963A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 23' Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 256 through 265 removed outlier: 4.186A pdb=" N ASP E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E 262 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS E 263 " --> pdb=" O CYS E 259 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS E 264 " --> pdb=" O GLN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 330 removed outlier: 3.882A pdb=" N GLU E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 436 through 445 Processing helix chain 'E' and resid 640 through 643 removed outlier: 3.966A pdb=" N GLU E 643 " --> pdb=" O GLU E 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 640 through 643' Processing helix chain 'E' and resid 863 through 869 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 256 through 267 removed outlier: 4.044A pdb=" N ASP F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 262 " --> pdb=" O PHE F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 330 No H-bonds generated for 'chain 'F' and resid 328 through 330' Processing helix chain 'F' and resid 351 through 358 removed outlier: 4.702A pdb=" N GLU F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 436 through 445 Processing helix chain 'F' and resid 639 through 643 removed outlier: 4.059A pdb=" N GLU F 643 " --> pdb=" O GLU F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 863 through 869 Processing sheet with id= A, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.676A pdb=" N GLN E 34 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 120 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N HIS E 144 " --> pdb=" O ILE E 119 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 246 through 248 Processing sheet with id= C, first strand: chain 'E' and resid 278 through 280 Processing sheet with id= D, first strand: chain 'E' and resid 318 through 321 removed outlier: 6.835A pdb=" N SER E 339 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE E 321 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE E 341 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG E 371 " --> pdb=" O ILE E 342 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 550 through 553 removed outlier: 3.589A pdb=" N MET E 553 " --> pdb=" O ILE E 485 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 479 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 488 " --> pdb=" O TYR E 477 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.610A pdb=" N THR E 530 " --> pdb=" O TYR E 507 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE E 503 " --> pdb=" O ILE E 534 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE E 564 " --> pdb=" O ILE E 586 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 602 through 605 Processing sheet with id= H, first strand: chain 'E' and resid 627 through 634 removed outlier: 3.707A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS E 786 " --> pdb=" O HIS E 627 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 819 through 822 removed outlier: 3.529A pdb=" N VAL E 828 " --> pdb=" O LEU E 874 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 901 through 904 Processing sheet with id= K, first strand: chain 'E' and resid 6 through 8 removed outlier: 7.265A pdb=" N CYS E 8 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE E 29 " --> pdb=" O CYS E 8 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.771A pdb=" N GLN F 34 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 95 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU F 120 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS F 144 " --> pdb=" O ILE F 119 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 246 through 248 Processing sheet with id= N, first strand: chain 'F' and resid 278 through 280 Processing sheet with id= O, first strand: chain 'F' and resid 340 through 342 removed outlier: 3.510A pdb=" N ARG F 371 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 550 through 553 Processing sheet with id= Q, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.520A pdb=" N THR F 530 " --> pdb=" O TYR F 507 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 503 " --> pdb=" O ILE F 534 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY F 502 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 564 " --> pdb=" O ILE F 586 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 602 through 605 removed outlier: 3.512A pdb=" N LEU F 768 " --> pdb=" O LEU F 613 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 627 through 634 removed outlier: 3.868A pdb=" N TYR F 779 " --> pdb=" O ALA F 803 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 803 " --> pdb=" O TYR F 779 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 781 " --> pdb=" O VAL F 801 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 799 " --> pdb=" O LEU F 783 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 819 through 822 removed outlier: 3.595A pdb=" N VAL F 828 " --> pdb=" O LEU F 874 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 856 through 859 removed outlier: 3.574A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL F 843 " --> pdb=" O THR F 889 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR F 889 " --> pdb=" O VAL F 843 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR F 845 " --> pdb=" O ARG F 887 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG F 887 " --> pdb=" O TYR F 845 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL F 847 " --> pdb=" O ARG F 885 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG F 885 " --> pdb=" O VAL F 847 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR F 849 " --> pdb=" O SER F 883 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER F 883 " --> pdb=" O TYR F 849 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ARG F 851 " --> pdb=" O ASN F 881 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASN F 881 " --> pdb=" O ARG F 851 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 6 through 8 removed outlier: 7.203A pdb=" N CYS F 8 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE F 29 " --> pdb=" O CYS F 8 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 501 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for UD residue Warning, Cannot make NA restraints for UD residue Warning, Cannot make NA restraints for UD residue Warning, Cannot make NA restraints for UD residue Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 6.57 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: 2234 1.31 - 1.44: 4233 1.44 - 1.58: 7732 1.58 - 1.71: 116 1.71 - 1.84: 134 Bond restraints: 14449 Sorted by residual: bond pdb=" O4' AF2 H 12 " pdb=" C1' AF2 H 12 " ideal model delta sigma weight residual 1.599 1.300 0.299 2.00e-02 2.50e+03 2.24e+02 bond pdb=" O4' AF2 G 12 " pdb=" C1' AF2 G 12 " ideal model delta sigma weight residual 1.599 1.300 0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" O4' AF2 G 19 " pdb=" C1' AF2 G 19 " ideal model delta sigma weight residual 1.599 1.301 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" O4' AF2 H 19 " pdb=" C1' AF2 H 19 " ideal model delta sigma weight residual 1.599 1.301 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" O4' AF2 H 2 " pdb=" C1' AF2 H 2 " ideal model delta sigma weight residual 1.599 1.301 0.298 2.00e-02 2.50e+03 2.22e+02 ... (remaining 14444 not shown) Histogram of bond angle deviations from ideal: 96.85 - 105.80: 564 105.80 - 114.75: 8475 114.75 - 123.70: 10034 123.70 - 132.65: 698 132.65 - 141.59: 41 Bond angle restraints: 19812 Sorted by residual: angle pdb=" N LYS E 484 " pdb=" CA LYS E 484 " pdb=" C LYS E 484 " ideal model delta sigma weight residual 108.90 118.36 -9.46 1.63e+00 3.76e-01 3.37e+01 angle pdb=" C LEU F 599 " pdb=" N ASP F 600 " pdb=" CA ASP F 600 " ideal model delta sigma weight residual 122.83 128.75 -5.92 1.08e+00 8.57e-01 3.01e+01 angle pdb=" C1' OMG H 13 " pdb=" N9 OMG H 13 " pdb=" C4 OMG H 13 " ideal model delta sigma weight residual 108.29 124.44 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C1' OMG G 13 " pdb=" N9 OMG G 13 " pdb=" C4 OMG G 13 " ideal model delta sigma weight residual 108.29 124.36 -16.07 3.00e+00 1.11e-01 2.87e+01 angle pdb=" CA CYS F 786 " pdb=" CB CYS F 786 " pdb=" SG CYS F 786 " ideal model delta sigma weight residual 114.40 126.37 -11.97 2.30e+00 1.89e-01 2.71e+01 ... (remaining 19807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 8065 35.63 - 71.27: 289 71.27 - 106.90: 32 106.90 - 142.53: 2 142.53 - 178.16: 6 Dihedral angle restraints: 8394 sinusoidal: 3736 harmonic: 4658 Sorted by residual: dihedral pdb=" CA PRO F 243 " pdb=" C PRO F 243 " pdb=" N PRO F 244 " pdb=" CA PRO F 244 " ideal model delta harmonic sigma weight residual 180.00 134.59 45.41 0 5.00e+00 4.00e-02 8.25e+01 dihedral pdb=" CB CYS E 435 " pdb=" SG CYS E 435 " pdb=" SG CYS E 468 " pdb=" CB CYS E 468 " ideal model delta sinusoidal sigma weight residual 93.00 11.79 81.21 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CA PRO E 243 " pdb=" C PRO E 243 " pdb=" N PRO E 244 " pdb=" CA PRO E 244 " ideal model delta harmonic sigma weight residual 180.00 135.08 44.92 0 5.00e+00 4.00e-02 8.07e+01 ... (remaining 8391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1727 0.079 - 0.158: 314 0.158 - 0.238: 28 0.238 - 0.317: 11 0.317 - 0.396: 5 Chirality restraints: 2085 Sorted by residual: chirality pdb=" C3' AF2 G 12 " pdb=" C4' AF2 G 12 " pdb=" O3' AF2 G 12 " pdb=" C2' AF2 G 12 " both_signs ideal model delta sigma weight residual False -2.47 -2.07 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C3' AF2 H 12 " pdb=" C4' AF2 H 12 " pdb=" O3' AF2 H 12 " pdb=" C2' AF2 H 12 " both_signs ideal model delta sigma weight residual False -2.47 -2.08 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C3' DUZ H 14 " pdb=" C4' DUZ H 14 " pdb=" O3' DUZ H 14 " pdb=" C2' DUZ H 14 " both_signs ideal model delta sigma weight residual False -2.39 -2.01 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2082 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG H 13 " 0.046 2.00e-02 2.50e+03 5.93e-01 7.90e+03 pdb=" C4' OMG H 13 " 0.442 2.00e-02 2.50e+03 pdb=" O4' OMG H 13 " 0.641 2.00e-02 2.50e+03 pdb=" C3' OMG H 13 " -0.589 2.00e-02 2.50e+03 pdb=" O3' OMG H 13 " -0.617 2.00e-02 2.50e+03 pdb=" C2' OMG H 13 " -0.188 2.00e-02 2.50e+03 pdb=" O2' OMG H 13 " 0.955 2.00e-02 2.50e+03 pdb=" C1' OMG H 13 " 0.220 2.00e-02 2.50e+03 pdb=" N9 OMG H 13 " -0.910 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG G 13 " -0.046 2.00e-02 2.50e+03 5.93e-01 7.90e+03 pdb=" C4' OMG G 13 " -0.443 2.00e-02 2.50e+03 pdb=" O4' OMG G 13 " -0.640 2.00e-02 2.50e+03 pdb=" C3' OMG G 13 " 0.589 2.00e-02 2.50e+03 pdb=" O3' OMG G 13 " 0.617 2.00e-02 2.50e+03 pdb=" C2' OMG G 13 " 0.188 2.00e-02 2.50e+03 pdb=" O2' OMG G 13 " -0.955 2.00e-02 2.50e+03 pdb=" C1' OMG G 13 " -0.220 2.00e-02 2.50e+03 pdb=" N9 OMG G 13 " 0.911 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG G 11 " -0.599 2.00e-02 2.50e+03 4.71e-01 4.99e+03 pdb=" C4' OMG G 11 " 0.250 2.00e-02 2.50e+03 pdb=" O4' OMG G 11 " 0.353 2.00e-02 2.50e+03 pdb=" C3' OMG G 11 " -0.246 2.00e-02 2.50e+03 pdb=" O3' OMG G 11 " 0.833 2.00e-02 2.50e+03 pdb=" C2' OMG G 11 " -0.599 2.00e-02 2.50e+03 pdb=" O2' OMG G 11 " -0.435 2.00e-02 2.50e+03 pdb=" C1' OMG G 11 " 0.378 2.00e-02 2.50e+03 pdb=" N9 OMG G 11 " 0.065 2.00e-02 2.50e+03 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1870 2.76 - 3.29: 12668 3.29 - 3.83: 23934 3.83 - 4.36: 26749 4.36 - 4.90: 43378 Nonbonded interactions: 108599 Sorted by model distance: nonbonded pdb=" O5' 85Y H 10 " pdb=" O4' 85Y H 10 " model vdw 2.222 2.432 nonbonded pdb=" O5' 85Y G 10 " pdb=" O4' 85Y G 10 " model vdw 2.222 2.432 nonbonded pdb=" O3' AF2 G 2 " pdb=" F AF2 G 2 " model vdw 2.269 2.392 nonbonded pdb=" O3' AF2 H 2 " pdb=" F AF2 H 2 " model vdw 2.269 2.392 nonbonded pdb=" OG SER F 339 " pdb=" O TYR F 367 " model vdw 2.292 2.440 ... (remaining 108594 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 'E' and (resid 1 through 143 or resid 145 through 649 or resid 756 throug \ h 907)) selection = (chain 'F' and (resid 1 through 143 or resid 145 through 907)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 7.200 Check model and map are aligned: 0.060 Set scattering table: 0.120 Process input model: 46.720 Find NCS groups from input model: 0.830 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.019 0.299 14449 Z= 1.049 Angle : 1.341 21.294 19812 Z= 0.612 Chirality : 0.064 0.396 2085 Planarity : 0.026 0.593 2401 Dihedral : 17.922 178.164 5284 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 7.06 % Twisted General : 0.07 % 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: -3.94 (0.18), residues: 1582 helix: -4.26 (0.25), residues: 97 sheet: -1.91 (0.27), residues: 332 loop : -2.90 (0.15), residues: 1153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.443 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 outliers start: 5 outliers final: 2 residues processed: 155 average time/residue: 0.2879 time to fit residues: 63.2410 Evaluate side-chains 78 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1167 time to fit residues: 2.4270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN E 263 HIS E 407 ASN E 440 HIS E 547 ASN E 622 ASN E 820 HIS ** E 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN F 152 ASN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 HIS F 407 ASN F 431 ASN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 547 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 14449 Z= 0.283 Angle : 1.131 19.208 19812 Z= 0.568 Chirality : 0.052 0.484 2085 Planarity : 0.008 0.121 2401 Dihedral : 19.685 165.419 2142 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 2.35 % 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: -3.54 (0.19), residues: 1582 helix: -3.49 (0.35), residues: 112 sheet: -1.72 (0.26), residues: 349 loop : -2.62 (0.16), residues: 1121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.2408 time to fit residues: 36.8958 Evaluate side-chains 56 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 HIS ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 HIS ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 14449 Z= 0.296 Angle : 1.071 18.667 19812 Z= 0.545 Chirality : 0.050 0.282 2085 Planarity : 0.008 0.122 2401 Dihedral : 19.591 174.959 2142 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 2.35 % 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: -3.39 (0.19), residues: 1582 helix: -3.14 (0.37), residues: 117 sheet: -1.53 (0.28), residues: 323 loop : -2.56 (0.17), residues: 1142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.2415 time to fit residues: 31.6740 Evaluate side-chains 62 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 GLN E 407 ASN E 410 GLN E 440 HIS ** E 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN F 431 ASN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.084 14449 Z= 0.462 Angle : 1.173 17.896 19812 Z= 0.587 Chirality : 0.053 0.293 2085 Planarity : 0.009 0.126 2401 Dihedral : 19.750 179.361 2142 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 4.71 % 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: -3.35 (0.19), residues: 1582 helix: -2.95 (0.42), residues: 104 sheet: -1.69 (0.26), residues: 354 loop : -2.51 (0.17), residues: 1124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.2828 time to fit residues: 33.7857 Evaluate side-chains 53 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.0570 chunk 88 optimal weight: 0.8980 chunk 2 optimal weight: 0.0010 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 0.0470 chunk 140 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS E 407 ASN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 14449 Z= 0.172 Angle : 1.027 18.697 19812 Z= 0.529 Chirality : 0.048 0.278 2085 Planarity : 0.008 0.118 2401 Dihedral : 19.364 178.121 2142 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 2.35 % Twisted General : 0.07 % 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: -3.07 (0.19), residues: 1582 helix: -2.97 (0.38), residues: 117 sheet: -1.30 (0.27), residues: 337 loop : -2.33 (0.17), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2115 time to fit residues: 31.7338 Evaluate side-chains 57 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 30 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 overall best weight: 1.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 407 ASN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 ASN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14449 Z= 0.207 Angle : 1.001 18.402 19812 Z= 0.516 Chirality : 0.047 0.260 2085 Planarity : 0.008 0.120 2401 Dihedral : 19.251 179.175 2142 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 3.53 % 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: -2.84 (0.20), residues: 1582 helix: -2.69 (0.44), residues: 104 sheet: -1.14 (0.28), residues: 325 loop : -2.20 (0.17), residues: 1153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2161 time to fit residues: 27.3223 Evaluate side-chains 56 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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: 50.7431 > 50: distance: 64 - 68: 22.333 distance: 68 - 69: 13.740 distance: 69 - 70: 7.403 distance: 69 - 72: 7.285 distance: 70 - 71: 13.854 distance: 70 - 77: 10.905 distance: 72 - 73: 19.479 distance: 73 - 74: 21.513 distance: 74 - 75: 13.301 distance: 74 - 76: 4.049 distance: 77 - 78: 11.467 distance: 77 - 83: 3.549 distance: 78 - 79: 11.106 distance: 78 - 81: 5.768 distance: 79 - 80: 16.312 distance: 79 - 84: 15.238 distance: 81 - 82: 15.739 distance: 82 - 83: 23.374 distance: 84 - 85: 7.513 distance: 85 - 86: 5.750 distance: 85 - 88: 6.954 distance: 86 - 87: 8.374 distance: 86 - 93: 8.050 distance: 88 - 89: 14.929 distance: 89 - 90: 12.768 distance: 90 - 91: 15.257 distance: 91 - 92: 8.569 distance: 93 - 94: 5.759 distance: 94 - 95: 18.109 distance: 94 - 97: 16.683 distance: 95 - 96: 14.026 distance: 95 - 102: 13.271 distance: 97 - 98: 14.263 distance: 98 - 99: 10.703 distance: 99 - 100: 15.496 distance: 99 - 101: 3.314 distance: 102 - 103: 15.792 distance: 102 - 108: 34.960 distance: 103 - 104: 7.684 distance: 103 - 106: 29.298 distance: 104 - 105: 16.422 distance: 104 - 109: 8.844 distance: 106 - 107: 26.784 distance: 107 - 108: 8.913 distance: 109 - 110: 9.208 distance: 110 - 111: 5.458 distance: 110 - 113: 18.453 distance: 111 - 112: 18.520 distance: 113 - 114: 13.197 distance: 114 - 115: 6.358 distance: 114 - 116: 6.411 distance: 117 - 118: 11.152 distance: 118 - 119: 8.206 distance: 119 - 120: 3.555 distance: 119 - 121: 5.880 distance: 122 - 123: 11.677 distance: 122 - 125: 9.200 distance: 123 - 124: 9.437 distance: 123 - 129: 7.976 distance: 125 - 126: 23.704 distance: 126 - 127: 23.825 distance: 126 - 128: 12.149 distance: 129 - 130: 5.093 distance: 130 - 131: 5.033 distance: 130 - 133: 5.781 distance: 131 - 132: 9.913 distance: 131 - 137: 12.320 distance: 133 - 134: 9.378 distance: 133 - 135: 25.587 distance: 134 - 136: 16.244 distance: 137 - 138: 5.395 distance: 138 - 141: 12.003 distance: 139 - 140: 5.046 distance: 139 - 144: 5.827 distance: 141 - 142: 14.127 distance: 141 - 143: 13.613