Starting phenix.real_space_refine on Fri Feb 16 05:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/02_2024/7yq6_34021_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/02_2024/7yq6_34021.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/02_2024/7yq6_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_34021/02_2024/7yq6_34021_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/02_2024/7yq6_34021_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/02_2024/7yq6_34021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/02_2024/7yq6_34021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/02_2024/7yq6_34021_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq6_34021/02_2024/7yq6_34021_updated.pdb" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 13.19, per 1000 atoms: 0.94 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: 5.72 Conformation dependent library (CDL) restraints added in 4.4 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: 6.38 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: 3.97 Time building geometry restraints manager: 6.19 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: 8181 35.63 - 71.27: 341 71.27 - 106.90: 40 106.90 - 142.53: 4 142.53 - 178.16: 8 Dihedral angle restraints: 8574 sinusoidal: 3916 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 8571 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 6.310 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 49.870 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.230 ------------------------------------------------------------------------------- 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 : 19.259 178.164 5464 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 % Allowed : 5.05 % Favored : 94.60 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 897 HIS 0.005 0.001 HIS F 187 PHE 0.020 0.002 PHE F 776 TYR 0.015 0.002 TYR E 904 ARG 0.017 0.001 ARG E 65 *********************** 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 : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 408 LEU cc_start: 0.9164 (mm) cc_final: 0.8846 (mp) REVERT: F 98 MET cc_start: 0.9084 (mmp) cc_final: 0.8780 (mmp) REVERT: F 552 LEU cc_start: 0.9273 (tp) cc_final: 0.8887 (tt) outliers start: 5 outliers final: 2 residues processed: 155 average time/residue: 0.2940 time to fit residues: 64.8346 Evaluate side-chains 79 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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: 0.8980 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: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN E 148 ASN E 263 HIS E 407 ASN E 440 HIS E 547 ASN E 622 ASN ** 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: 0.7904 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14449 Z= 0.285 Angle : 1.128 19.291 19812 Z= 0.567 Chirality : 0.052 0.438 2085 Planarity : 0.008 0.121 2401 Dihedral : 22.123 164.925 2322 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.89 % 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: -3.51 (0.35), residues: 112 sheet: -1.71 (0.26), residues: 349 loop : -2.63 (0.16), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 412 HIS 0.007 0.001 HIS F 829 PHE 0.020 0.002 PHE F 776 TYR 0.026 0.002 TYR E 477 ARG 0.008 0.000 ARG E 554 *********************** 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 98 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 LEU cc_start: 0.9073 (tp) cc_final: 0.8850 (tt) REVERT: E 408 LEU cc_start: 0.9182 (mm) cc_final: 0.8895 (mp) REVERT: E 594 ASN cc_start: 0.8746 (m-40) cc_final: 0.8507 (p0) REVERT: F 56 MET cc_start: 0.7367 (tpt) cc_final: 0.7102 (tpp) REVERT: F 98 MET cc_start: 0.9136 (mmp) cc_final: 0.8504 (mmp) REVERT: F 407 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6706 (t0) REVERT: F 552 LEU cc_start: 0.9366 (tp) cc_final: 0.9133 (tt) REVERT: F 768 LEU cc_start: 0.8554 (tp) cc_final: 0.8315 (tt) REVERT: F 783 LEU cc_start: 0.9481 (pt) cc_final: 0.9049 (tp) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.2345 time to fit residues: 36.2120 Evaluate side-chains 60 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** ** 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 440 HIS ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14449 Z= 0.214 Angle : 1.040 19.122 19812 Z= 0.533 Chirality : 0.049 0.274 2085 Planarity : 0.008 0.118 2401 Dihedral : 21.714 171.176 2322 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: -3.36 (0.19), residues: 1582 helix: -3.28 (0.36), residues: 117 sheet: -1.48 (0.27), residues: 341 loop : -2.53 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 414 HIS 0.006 0.001 HIS F 829 PHE 0.017 0.002 PHE F 776 TYR 0.018 0.001 TYR E 477 ARG 0.007 0.000 ARG F 118 *********************** 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 92 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 LEU cc_start: 0.8942 (mt) cc_final: 0.8677 (mt) REVERT: E 98 MET cc_start: 0.9126 (mmm) cc_final: 0.8697 (mmp) REVERT: E 101 LEU cc_start: 0.9026 (tp) cc_final: 0.8728 (tt) REVERT: E 363 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6743 (tt0) REVERT: E 408 LEU cc_start: 0.9224 (mm) cc_final: 0.8972 (mp) REVERT: F 56 MET cc_start: 0.7171 (tpt) cc_final: 0.6854 (tpt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2383 time to fit residues: 34.7141 Evaluate side-chains 67 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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: 0.9980 chunk 110 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 0.0670 chunk 98 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 410 GLN E 452 GLN ** E 833 GLN ** 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 313 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14449 Z= 0.340 Angle : 1.087 18.328 19812 Z= 0.551 Chirality : 0.050 0.266 2085 Planarity : 0.008 0.124 2401 Dihedral : 21.681 179.570 2322 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -3.28 (0.19), residues: 1582 helix: -3.04 (0.39), residues: 111 sheet: -1.48 (0.28), residues: 329 loop : -2.48 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 414 HIS 0.006 0.001 HIS F 275 PHE 0.048 0.002 PHE F 89 TYR 0.012 0.002 TYR E 492 ARG 0.005 0.001 ARG F 554 *********************** 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 81 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 408 LEU cc_start: 0.9272 (mm) cc_final: 0.8970 (mp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2348 time to fit residues: 30.7877 Evaluate side-chains 62 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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: 0.0030 chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 0.1980 chunk 64 optimal weight: 20.0000 chunk 133 optimal weight: 0.0170 chunk 108 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 0.0370 chunk 140 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.8508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 GLN ** 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 337 ASN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14449 Z= 0.182 Angle : 1.008 18.065 19812 Z= 0.521 Chirality : 0.048 0.255 2085 Planarity : 0.008 0.118 2401 Dihedral : 21.409 177.481 2322 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.07 % Allowed : 1.38 % Favored : 98.55 % 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: -3.03 (0.19), residues: 1582 helix: -2.97 (0.38), residues: 117 sheet: -1.22 (0.28), residues: 327 loop : -2.32 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 414 HIS 0.009 0.001 HIS F 199 PHE 0.018 0.002 PHE F 89 TYR 0.014 0.001 TYR E 477 ARG 0.009 0.000 ARG E 271 *********************** 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: 1 poor density : 89 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 LEU cc_start: 0.8992 (mt) cc_final: 0.8639 (mt) REVERT: E 363 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6825 (tt0) REVERT: E 408 LEU cc_start: 0.9229 (mm) cc_final: 0.8968 (mp) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2196 time to fit residues: 32.4049 Evaluate side-chains 62 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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: 3.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 51 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 overall best weight: 1.1940 ------------------------------------------------------------------------------- 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** ** 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 594 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3197 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= 0.193 Angle : 0.992 18.116 19812 Z= 0.513 Chirality : 0.048 0.245 2085 Planarity : 0.008 0.119 2401 Dihedral : 21.244 178.050 2322 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -2.88 (0.20), residues: 1582 helix: -2.69 (0.41), residues: 117 sheet: -1.10 (0.28), residues: 327 loop : -2.23 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 414 HIS 0.005 0.001 HIS F 829 PHE 0.021 0.002 PHE F 89 TYR 0.009 0.001 TYR E 507 ARG 0.003 0.000 ARG F 386 *********************** 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 89 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 LEU cc_start: 0.8982 (mt) cc_final: 0.8614 (mt) REVERT: E 374 TYR cc_start: 0.7255 (t80) cc_final: 0.6926 (t80) REVERT: E 408 LEU cc_start: 0.9255 (mm) cc_final: 0.8992 (mp) REVERT: F 246 TYR cc_start: 0.8000 (m-80) cc_final: 0.7762 (m-80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2295 time to fit residues: 33.4553 Evaluate side-chains 61 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS E 406 GLN E 407 ASN E 784 GLN ** 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 313 HIS ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN F 431 ASN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14449 Z= 0.375 Angle : 1.098 17.701 19812 Z= 0.555 Chirality : 0.051 0.269 2085 Planarity : 0.008 0.124 2401 Dihedral : 21.435 176.790 2322 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -2.90 (0.20), residues: 1582 helix: -2.70 (0.42), residues: 105 sheet: -1.29 (0.27), residues: 334 loop : -2.20 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 414 HIS 0.006 0.001 HIS F 313 PHE 0.042 0.002 PHE F 89 TYR 0.019 0.002 TYR F 587 ARG 0.007 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 7 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 78 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.8761 (mmm) cc_final: 0.8556 (mmm) REVERT: E 408 LEU cc_start: 0.9321 (mm) cc_final: 0.9072 (mp) REVERT: F 56 MET cc_start: 0.7013 (tpt) cc_final: 0.6555 (tpt) REVERT: F 553 MET cc_start: 0.8257 (mtp) cc_final: 0.7787 (mtp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2202 time to fit residues: 28.3495 Evaluate side-chains 55 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 784 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14449 Z= 0.187 Angle : 1.001 18.228 19812 Z= 0.517 Chirality : 0.048 0.261 2085 Planarity : 0.008 0.119 2401 Dihedral : 21.157 175.518 2322 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -2.68 (0.20), residues: 1582 helix: -2.59 (0.43), residues: 104 sheet: -0.94 (0.29), residues: 317 loop : -2.11 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 414 HIS 0.008 0.001 HIS F 199 PHE 0.016 0.002 PHE F 89 TYR 0.010 0.001 TYR E 127 ARG 0.003 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 8 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: 0 poor density : 83 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 LEU cc_start: 0.8927 (mt) cc_final: 0.8518 (mt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2177 time to fit residues: 29.8330 Evaluate side-chains 57 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS E 784 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14449 Z= 0.234 Angle : 1.009 17.813 19812 Z= 0.519 Chirality : 0.049 0.262 2085 Planarity : 0.008 0.121 2401 Dihedral : 21.080 175.564 2322 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -2.63 (0.20), residues: 1582 helix: -2.43 (0.44), residues: 104 sheet: -0.94 (0.29), residues: 316 loop : -2.06 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 414 HIS 0.005 0.001 HIS F 829 PHE 0.024 0.002 PHE F 89 TYR 0.010 0.001 TYR E 127 ARG 0.004 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 9 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 81 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 LEU cc_start: 0.8990 (mt) cc_final: 0.8584 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2076 time to fit residues: 28.3873 Evaluate side-chains 57 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 chunk 102 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS ** 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 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14449 Z= 0.241 Angle : 1.005 17.547 19812 Z= 0.519 Chirality : 0.049 0.265 2085 Planarity : 0.008 0.121 2401 Dihedral : 21.026 175.478 2322 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: -2.63 (0.20), residues: 1582 helix: -2.50 (0.43), residues: 105 sheet: -0.96 (0.29), residues: 316 loop : -2.05 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 414 HIS 0.005 0.001 HIS F 829 PHE 0.023 0.002 PHE F 89 TYR 0.013 0.001 TYR F 507 ARG 0.004 0.000 ARG F 118 ********************** REFINEMENT MACRO_CYCLE 10 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: 0 poor density : 77 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 LEU cc_start: 0.8973 (mt) cc_final: 0.8567 (mt) REVERT: E 374 TYR cc_start: 0.7443 (t80) cc_final: 0.6991 (t80) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2025 time to fit residues: 26.4042 Evaluate side-chains 56 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.091301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.066608 restraints weight = 123229.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068929 restraints weight = 69587.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069069 restraints weight = 36581.888| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14449 Z= 0.202 Angle : 0.990 17.611 19812 Z= 0.513 Chirality : 0.048 0.265 2085 Planarity : 0.008 0.120 2401 Dihedral : 20.937 175.284 2322 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -2.55 (0.20), residues: 1582 helix: -2.40 (0.45), residues: 104 sheet: -0.88 (0.29), residues: 316 loop : -2.01 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 414 HIS 0.005 0.001 HIS E 199 PHE 0.019 0.002 PHE F 89 TYR 0.011 0.001 TYR F 507 ARG 0.004 0.000 ARG F 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.93 seconds wall clock time: 45 minutes 46.28 seconds (2746.28 seconds total)