Starting phenix.real_space_refine (version: dev) on Tue Dec 13 06:36:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guy_34281/12_2022/8guy_34281.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guy_34281/12_2022/8guy_34281.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guy_34281/12_2022/8guy_34281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guy_34281/12_2022/8guy_34281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guy_34281/12_2022/8guy_34281.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guy_34281/12_2022/8guy_34281.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= 0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E ARG 331": "NH1" <-> "NH2" Residue "E GLU 362": "OE1" <-> "OE2" Residue "E GLU 363": "OE1" <-> "OE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 453": "OE1" <-> "OE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 522": "OD1" <-> "OD2" Residue "E ASP 542": "OD1" <-> "OD2" Residue "E ARG 576": "NH1" <-> "NH2" Residue "E TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 706": "OE1" <-> "OE2" Residue "E ARG 717": "NH1" <-> "NH2" Residue "E GLU 766": "OE1" <-> "OE2" Residue "E GLU 808": "OE1" <-> "OE2" Residue "E ASP 854": "OD1" <-> "OD2" Residue "E ARG 863": "NH1" <-> "NH2" Residue "E TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 907": "OD1" <-> "OD2" Residue "F TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F GLU 362": "OE1" <-> "OE2" Residue "F TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F GLU 453": "OE1" <-> "OE2" Residue "F PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 496": "OD1" <-> "OD2" Residue "F ASP 522": "OD1" <-> "OD2" Residue "F ASP 542": "OD1" <-> "OD2" Residue "F TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 576": "NH1" <-> "NH2" Residue "F TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F ARG 717": "NH1" <-> "NH2" Residue "F GLU 766": "OE1" <-> "OE2" Residue "F GLU 824": "OE1" <-> "OE2" Residue "F GLU 855": "OE1" <-> "OE2" Residue "F GLU 856": "OE1" <-> "OE2" Residue "F ARG 863": "NH1" <-> "NH2" Residue "F TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 907": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 14222 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 6736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 bond proxies already assigned to first conformer: 6887 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "C" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "F" Number of atoms: 6736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 bond proxies already assigned to first conformer: 6887 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR B 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 26 " occ=0.50 residue: pdb=" N ATYR D 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 26 " occ=0.50 Time building chain proxies: 14.57, per 1000 atoms: 1.02 Number of scatterers: 14222 At special positions: 0 Unit cell: (119.84, 132.68, 174.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 2646 8.00 N 2456 7.00 C 9006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.02 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 524 " - pdb=" SG CYS F 524 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 683 " - pdb=" SG CYS F 683 " distance=2.04 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.04 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.04 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.02 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.02 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.02 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=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 860 " distance=2.03 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.02 Conformation dependent library (CDL) restraints added in 4.2 seconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 32 sheets defined 15.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.923A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.096A pdb=" N ILE E 131 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 137 removed outlier: 4.034A pdb=" N ILE E 136 " --> pdb=" O ASP E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.534A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU E 262 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS E 263 " --> pdb=" O CYS E 259 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 413 through 417 removed outlier: 3.526A pdb=" N HIS E 417 " --> pdb=" O TRP E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 444 removed outlier: 3.851A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 644 removed outlier: 3.592A pdb=" N PHE E 642 " --> pdb=" O SER E 639 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU E 643 " --> pdb=" O GLU E 640 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 644 " --> pdb=" O LEU E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 714 removed outlier: 3.675A pdb=" N GLU E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN E 711 " --> pdb=" O ASP E 707 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 712 " --> pdb=" O TYR E 708 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 714 " --> pdb=" O HIS E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 813 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.532A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.070A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.531A pdb=" N GLU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 10 through 19 removed outlier: 4.165A pdb=" N TYR D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 132 through 137 removed outlier: 4.021A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 152 removed outlier: 3.509A pdb=" N ASN F 152 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.661A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU F 262 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 413 through 417 removed outlier: 3.510A pdb=" N HIS F 417 " --> pdb=" O TRP F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.877A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS F 440 " --> pdb=" O LEU F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 644 removed outlier: 3.530A pdb=" N PHE F 642 " --> pdb=" O SER F 639 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU F 643 " --> pdb=" O GLU F 640 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 644 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 714 removed outlier: 3.642A pdb=" N GLU F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR F 708 " --> pdb=" O THR F 704 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 711 " --> pdb=" O ASP F 707 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 712 " --> pdb=" O TYR F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 813 Processing helix chain 'F' and resid 862 through 870 Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 8 removed outlier: 6.954A pdb=" N GLU E 6 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE E 29 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N CYS E 8 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 82 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.832A pdb=" N MET E 11 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU E 36 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE E 13 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET E 38 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 64 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 37 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 66 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU E 61 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE E 96 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E 63 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLU E 120 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 95 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.362A pdb=" N ALA E 227 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN E 215 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N CYS E 225 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'E' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 312 removed outlier: 3.856A pdb=" N ILE E 364 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 318 through 321 removed outlier: 3.884A pdb=" N LYS E 319 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 341 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AB2, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.678A pdb=" N ILE E 564 " --> pdb=" O ILE E 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 599 through 605 removed outlier: 5.491A pdb=" N ASP E 600 " --> pdb=" O LYS E 616 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS E 616 " --> pdb=" O ASP E 600 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 612 " --> pdb=" O VAL E 604 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 611 " --> pdb=" O ILE E 770 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 4.124A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 819 through 822 removed outlier: 3.543A pdb=" N VAL E 828 " --> pdb=" O LEU E 874 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 856 through 859 removed outlier: 3.548A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 886 " --> pdb=" O TRP E 897 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP E 897 " --> pdb=" O ILE E 886 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA E 888 " --> pdb=" O GLY E 895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 856 through 859 removed outlier: 3.548A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 903 " --> pdb=" O TYR E 882 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 6 through 8 removed outlier: 6.954A pdb=" N GLU F 6 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE F 29 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS F 8 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 11 through 14 removed outlier: 3.658A pdb=" N PHE F 64 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 37 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU F 61 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N PHE F 96 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU F 63 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLU F 120 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE F 95 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.237A pdb=" N ALA F 227 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASN F 215 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N CYS F 225 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AC3, first strand: chain 'F' and resid 278 through 280 Processing sheet with id=AC4, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AC5, first strand: chain 'F' and resid 311 through 312 removed outlier: 3.801A pdb=" N ILE F 364 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 318 through 321 removed outlier: 3.777A pdb=" N LYS F 319 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE F 341 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG F 371 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AC8, first strand: chain 'F' and resid 475 through 480 Processing sheet with id=AC9, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.530A pdb=" N LYS F 508 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 564 " --> pdb=" O ILE F 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 599 through 605 removed outlier: 5.430A pdb=" N ASP F 600 " --> pdb=" O LYS F 616 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS F 616 " --> pdb=" O ASP F 600 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE F 612 " --> pdb=" O VAL F 604 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 611 " --> pdb=" O ILE F 770 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 761 through 762 removed outlier: 3.680A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 819 through 822 removed outlier: 3.545A pdb=" N VAL F 828 " --> pdb=" O LEU F 874 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 857 through 859 removed outlier: 3.586A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 886 " --> pdb=" O TRP F 897 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TRP F 897 " --> pdb=" O ILE F 886 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA F 888 " --> pdb=" O GLY F 895 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 857 through 859 removed outlier: 3.586A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 903 " --> pdb=" O TYR F 882 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 789 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.28 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4683 1.35 - 1.48: 3636 1.48 - 1.60: 6121 1.60 - 1.73: 0 1.73 - 1.85: 136 Bond restraints: 14576 Sorted by residual: bond pdb=" CB GLU F 637 " pdb=" CG GLU F 637 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" CB CYS F 435 " pdb=" SG CYS F 435 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CB GLU E 637 " pdb=" CG GLU E 637 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB CYS E 435 " pdb=" SG CYS E 435 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.73e+00 bond pdb=" CA THR E 578 " pdb=" CB THR E 578 " ideal model delta sigma weight residual 1.527 1.553 -0.026 1.61e-02 3.86e+03 2.51e+00 ... (remaining 14571 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.03: 363 106.03 - 113.04: 7485 113.04 - 120.05: 5364 120.05 - 127.06: 6349 127.06 - 134.07: 209 Bond angle restraints: 19770 Sorted by residual: angle pdb=" N VAL E 445 " pdb=" CA VAL E 445 " pdb=" C VAL E 445 " ideal model delta sigma weight residual 112.96 105.76 7.20 1.00e+00 1.00e+00 5.18e+01 angle pdb=" C ARG E 577 " pdb=" N THR E 578 " pdb=" CA THR E 578 " ideal model delta sigma weight residual 122.82 128.40 -5.58 1.42e+00 4.96e-01 1.54e+01 angle pdb=" C ARG F 14 " pdb=" N ASN F 15 " pdb=" CA ASN F 15 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N GLU E 808 " pdb=" CA GLU E 808 " pdb=" C GLU E 808 " ideal model delta sigma weight residual 110.53 115.59 -5.06 1.32e+00 5.74e-01 1.47e+01 angle pdb=" CA CYS F 308 " pdb=" CB CYS F 308 " pdb=" SG CYS F 308 " ideal model delta sigma weight residual 114.40 123.19 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 19765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7845 17.90 - 35.80: 830 35.80 - 53.70: 130 53.70 - 71.60: 47 71.60 - 89.51: 16 Dihedral angle restraints: 8868 sinusoidal: 3704 harmonic: 5164 Sorted by residual: 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 180.00 133.72 46.28 0 5.00e+00 4.00e-02 8.57e+01 dihedral pdb=" CB CYS F 647 " pdb=" SG CYS F 647 " pdb=" SG CYS F 860 " pdb=" CB CYS F 860 " ideal model delta sinusoidal sigma weight residual 93.00 176.28 -83.28 1 1.00e+01 1.00e-02 8.48e+01 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 180.00 134.03 45.97 0 5.00e+00 4.00e-02 8.45e+01 ... (remaining 8865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1654 0.065 - 0.131: 403 0.131 - 0.196: 67 0.196 - 0.262: 15 0.262 - 0.327: 1 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CB THR F 790 " pdb=" CA THR F 790 " pdb=" OG1 THR F 790 " pdb=" CG2 THR F 790 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA THR F 790 " pdb=" N THR F 790 " pdb=" C THR F 790 " pdb=" CB THR F 790 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE E 781 " pdb=" CA ILE E 781 " pdb=" CG1 ILE E 781 " pdb=" CG2 ILE E 781 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2137 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 243 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO F 244 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO F 244 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO F 244 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 243 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO E 244 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO E 244 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 244 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 242 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO F 243 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 243 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 243 " 0.047 5.00e-02 4.00e+02 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2977 2.78 - 3.31: 12547 3.31 - 3.84: 23562 3.84 - 4.37: 25822 4.37 - 4.90: 43345 Nonbonded interactions: 108253 Sorted by model distance: nonbonded pdb=" OD1 ASP E 59 " pdb=" OG SER E 85 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASP F 59 " pdb=" OG SER F 85 " model vdw 2.258 2.440 nonbonded pdb=" OG SER E 116 " pdb=" OD1 ASN E 143 " model vdw 2.299 2.440 nonbonded pdb=" OG SER F 116 " pdb=" OD1 ASN F 143 " model vdw 2.317 2.440 nonbonded pdb=" OG1 THR F 334 " pdb=" OE1 GLU F 362 " model vdw 2.333 2.440 ... (remaining 108248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 3 through 25 or resid 27)) selection = (chain 'D' and (resid 3 through 25 or resid 27)) } ncs_group { reference = (chain 'E' and (resid 1 through 143 or resid 145 through 907)) selection = (chain 'F' and (resid 1 through 143 or resid 145 through 907)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 9006 2.51 5 N 2456 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.490 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.120 Process input model: 49.200 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 14576 Z= 0.336 Angle : 1.005 11.587 19770 Z= 0.539 Chirality : 0.060 0.327 2140 Planarity : 0.007 0.112 2566 Dihedral : 14.547 89.506 5408 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % Twisted General : 0.12 % 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: -4.23 (0.17), residues: 1744 helix: -4.43 (0.16), residues: 216 sheet: -1.99 (0.27), residues: 316 loop : -2.92 (0.15), residues: 1212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2377 time to fit residues: 50.5135 Evaluate side-chains 75 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 30.0000 chunk 101 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 249 GLN E 282 ASN E 405 ASN E 431 ASN E 589 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 HIS F 32 HIS F 177 GLN F 249 GLN F 431 ASN F 589 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 833 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 14576 Z= 0.303 Angle : 0.726 6.771 19770 Z= 0.381 Chirality : 0.047 0.192 2140 Planarity : 0.006 0.099 2566 Dihedral : 6.654 59.760 1938 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -3.64 (0.18), residues: 1744 helix: -3.36 (0.24), residues: 210 sheet: -2.02 (0.26), residues: 352 loop : -2.51 (0.17), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2426 time to fit residues: 37.5833 Evaluate side-chains 67 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 171 optimal weight: 30.0000 chunk 140 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 53 optimal weight: 0.0170 chunk 126 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 627 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 14576 Z= 0.166 Angle : 0.629 6.772 19770 Z= 0.325 Chirality : 0.045 0.194 2140 Planarity : 0.005 0.103 2566 Dihedral : 5.975 58.252 1938 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -3.10 (0.19), residues: 1744 helix: -2.48 (0.31), residues: 196 sheet: -1.47 (0.27), residues: 334 loop : -2.31 (0.17), residues: 1214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2249 time to fit residues: 37.8905 Evaluate side-chains 68 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 140 optimal weight: 3.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 787 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14576 Z= 0.201 Angle : 0.615 6.648 19770 Z= 0.317 Chirality : 0.046 0.190 2140 Planarity : 0.005 0.105 2566 Dihedral : 5.768 56.586 1938 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.91 (0.19), residues: 1744 helix: -1.98 (0.33), residues: 208 sheet: -1.36 (0.28), residues: 334 loop : -2.24 (0.18), residues: 1202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2204 time to fit residues: 33.8113 Evaluate side-chains 64 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 143 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN E 547 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14576 Z= 0.190 Angle : 0.596 6.470 19770 Z= 0.306 Chirality : 0.045 0.190 2140 Planarity : 0.005 0.105 2566 Dihedral : 5.603 55.893 1938 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.81 (0.20), residues: 1744 helix: -1.82 (0.33), residues: 216 sheet: -1.28 (0.28), residues: 334 loop : -2.18 (0.18), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2352 time to fit residues: 34.5635 Evaluate side-chains 66 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 139 optimal weight: 0.0060 chunk 77 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 162 optimal weight: 5.9990 overall best weight: 0.5474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 405 ASN F 521 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 833 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 14576 Z= 0.149 Angle : 0.589 7.282 19770 Z= 0.299 Chirality : 0.045 0.187 2140 Planarity : 0.005 0.106 2566 Dihedral : 5.420 56.420 1938 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.61 (0.20), residues: 1744 helix: -1.67 (0.34), residues: 216 sheet: -1.12 (0.28), residues: 334 loop : -2.05 (0.18), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2766 time to fit residues: 43.5616 Evaluate side-chains 63 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 103 optimal weight: 0.0070 chunk 66 optimal weight: 0.7980 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN E 527 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 HIS ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14576 Z= 0.213 Angle : 0.610 6.883 19770 Z= 0.311 Chirality : 0.045 0.179 2140 Planarity : 0.005 0.106 2566 Dihedral : 5.410 54.324 1938 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: 1744 helix: -1.30 (0.37), residues: 194 sheet: -1.19 (0.27), residues: 354 loop : -2.04 (0.18), residues: 1196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2123 time to fit residues: 29.4583 Evaluate side-chains 57 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.4980 chunk 50 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 152 optimal weight: 10.0000 chunk 160 optimal weight: 0.2980 chunk 146 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 14576 Z= 0.145 Angle : 0.573 7.715 19770 Z= 0.291 Chirality : 0.044 0.177 2140 Planarity : 0.005 0.108 2566 Dihedral : 5.223 53.376 1938 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.39 (0.20), residues: 1744 helix: -1.28 (0.36), residues: 202 sheet: -1.04 (0.28), residues: 354 loop : -1.93 (0.18), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1923 time to fit residues: 28.2974 Evaluate side-chains 58 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 147 optimal weight: 0.0270 chunk 155 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 527 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14576 Z= 0.194 Angle : 0.588 7.353 19770 Z= 0.299 Chirality : 0.045 0.175 2140 Planarity : 0.005 0.107 2566 Dihedral : 5.229 50.747 1938 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.31 (0.20), residues: 1744 helix: -1.10 (0.37), residues: 194 sheet: -1.02 (0.28), residues: 350 loop : -1.87 (0.18), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.042 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2089 time to fit residues: 28.6263 Evaluate side-chains 55 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.3980 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 84 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14576 Z= 0.181 Angle : 0.580 6.889 19770 Z= 0.295 Chirality : 0.044 0.173 2140 Planarity : 0.005 0.108 2566 Dihedral : 5.186 49.040 1938 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.25 (0.20), residues: 1744 helix: -1.09 (0.37), residues: 194 sheet: -1.00 (0.28), residues: 350 loop : -1.82 (0.18), residues: 1200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2042 time to fit residues: 28.1874 Evaluate side-chains 57 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 0.0570 chunk 121 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** 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 = 0.3879 r_free = 0.3879 target = 0.090877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.064618 restraints weight = 187257.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.065635 restraints weight = 94903.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.066289 restraints weight = 56963.386| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 14576 Z= 0.137 Angle : 0.574 6.832 19770 Z= 0.290 Chirality : 0.044 0.179 2140 Planarity : 0.005 0.108 2566 Dihedral : 5.042 47.177 1938 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.21 (0.20), residues: 1744 helix: -1.28 (0.35), residues: 214 sheet: -0.90 (0.28), residues: 350 loop : -1.77 (0.18), residues: 1180 =============================================================================== Job complete usr+sys time: 2419.53 seconds wall clock time: 45 minutes 13.52 seconds (2713.52 seconds total)