Starting phenix.real_space_refine (version: dev) on Sat Feb 25 02:50:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/02_2023/7wv4_32845_updated.pdb" } resolution = 3.35 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= -0.006 sd= 1.057 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 Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 639": "OE1" <-> "OE2" Residue "C PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D GLU 456": "OE1" <-> "OE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24490 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1597 Classifications: {'RNA': 80} Modifications used: {'5*END': 1, 'rna3p_pyr': 80} Link IDs: {'rna3p': 79} Chain: "F" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1757 Classifications: {'RNA': 80} Modifications used: {'5*END': 1, 'rna3p': 80} Link IDs: {'rna3p': 79} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Time building chain proxies: 12.13, per 1000 atoms: 0.50 Number of scatterers: 24490 At special positions: 0 Unit cell: (98.5545, 113.215, 257.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 158 15.00 O 5080 8.00 N 4144 7.00 C 15040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 677 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 677 " distance=2.03 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 649 " - pdb=" SG CYS D 677 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.55 Conformation dependent library (CDL) restraints added in 3.0 seconds 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 16 sheets defined 9.1% alpha, 7.9% beta 0 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 9.04 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.611A pdb=" N ASP A 192 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN A 196 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 400 through 404 removed outlier: 4.378A pdb=" N SER A 403 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.610A pdb=" N ASP B 192 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE B 193 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN B 196 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 400 through 404 removed outlier: 4.378A pdb=" N SER B 403 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 627 through 630 No H-bonds generated for 'chain 'B' and resid 627 through 630' Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.611A pdb=" N ASP C 192 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE C 193 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 195 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN C 196 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 400 through 404 removed outlier: 4.378A pdb=" N SER C 403 " --> pdb=" O THR C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 523 through 525 No H-bonds generated for 'chain 'C' and resid 523 through 525' Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 627 through 630 No H-bonds generated for 'chain 'C' and resid 627 through 630' Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 655 through 662 Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.611A pdb=" N ASP D 192 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE D 193 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 195 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN D 196 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'D' and resid 400 through 404 removed outlier: 4.378A pdb=" N SER D 403 " --> pdb=" O THR D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 523 through 525 No H-bonds generated for 'chain 'D' and resid 523 through 525' Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 627 through 630 No H-bonds generated for 'chain 'D' and resid 627 through 630' Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 655 through 662 Processing helix chain 'D' and resid 681 through 683 No H-bonds generated for 'chain 'D' and resid 681 through 683' Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.618A pdb=" N VAL A 55 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A 79 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 103 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 127 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR A 151 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU A 175 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS A 201 " --> pdb=" O LEU A 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.322A pdb=" N ASN A 252 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N MET A 278 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR A 302 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR A 326 " --> pdb=" O PHE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 383 through 385 removed outlier: 6.104A pdb=" N ILE A 411 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 435 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU A 460 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 484 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 510 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 534 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE A 566 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 590 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER A 614 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU A 639 " --> pdb=" O LEU A 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 444 through 446 removed outlier: 6.140A pdb=" N TYR A 468 " --> pdb=" O GLN A 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.619A pdb=" N VAL B 55 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER B 79 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 103 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU B 127 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 151 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 175 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.322A pdb=" N ASN B 252 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N MET B 278 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR B 302 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 326 " --> pdb=" O PHE B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 383 through 385 removed outlier: 6.104A pdb=" N ILE B 411 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 435 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU B 460 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 534 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE B 566 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 590 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER B 614 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU B 639 " --> pdb=" O LEU B 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 444 through 446 removed outlier: 6.140A pdb=" N TYR B 468 " --> pdb=" O GLN B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 34 through 36 removed outlier: 6.618A pdb=" N VAL C 55 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 79 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 103 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU C 127 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 151 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU C 175 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS C 201 " --> pdb=" O LEU C 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 225 through 227 removed outlier: 6.322A pdb=" N ASN C 252 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N MET C 278 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR C 302 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR C 326 " --> pdb=" O PHE C 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 383 through 385 removed outlier: 6.103A pdb=" N ILE C 411 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 435 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 460 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG C 484 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 510 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 534 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 566 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 590 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER C 614 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU C 639 " --> pdb=" O LEU C 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 444 through 446 removed outlier: 6.140A pdb=" N TYR C 468 " --> pdb=" O GLN C 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 34 through 36 removed outlier: 6.618A pdb=" N VAL D 55 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D 79 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL D 103 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU D 127 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR D 151 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU D 175 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS D 201 " --> pdb=" O LEU D 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 225 through 227 removed outlier: 6.322A pdb=" N ASN D 252 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N MET D 278 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR D 302 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR D 326 " --> pdb=" O PHE D 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 383 through 385 removed outlier: 6.103A pdb=" N ILE D 411 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL D 435 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU D 460 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG D 484 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE D 510 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE D 534 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 566 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 590 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER D 614 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU D 639 " --> pdb=" O LEU D 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 444 through 446 removed outlier: 6.140A pdb=" N TYR D 468 " --> pdb=" O GLN D 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 52 hydrogen bonds defined for protein. 120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7019 1.34 - 1.45: 4710 1.45 - 1.57: 13191 1.57 - 1.69: 316 1.69 - 1.81: 100 Bond restraints: 25336 Sorted by residual: bond pdb=" C2 I F 63 " pdb=" N3 I F 63 " ideal model delta sigma weight residual 1.462 1.314 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" C2 I F 66 " pdb=" N3 I F 66 " ideal model delta sigma weight residual 1.462 1.314 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" C2 I F 68 " pdb=" N3 I F 68 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C2 I F 48 " pdb=" N3 I F 48 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C2 I F 65 " pdb=" N3 I F 65 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.42e+01 ... (remaining 25331 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.68: 1373 106.68 - 113.51: 14538 113.51 - 120.34: 8823 120.34 - 127.17: 9835 127.17 - 134.00: 559 Bond angle restraints: 35128 Sorted by residual: angle pdb=" C1' I F 64 " pdb=" N9 I F 64 " pdb=" C4 I F 64 " ideal model delta sigma weight residual 106.08 125.48 -19.40 3.00e+00 1.11e-01 4.18e+01 angle pdb=" C1' I F 63 " pdb=" N9 I F 63 " pdb=" C4 I F 63 " ideal model delta sigma weight residual 106.08 125.26 -19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" C1' I F 79 " pdb=" N9 I F 79 " pdb=" C4 I F 79 " ideal model delta sigma weight residual 106.08 125.00 -18.92 3.00e+00 1.11e-01 3.98e+01 angle pdb=" C1' I F 5 " pdb=" N9 I F 5 " pdb=" C4 I F 5 " ideal model delta sigma weight residual 106.08 124.92 -18.84 3.00e+00 1.11e-01 3.94e+01 angle pdb=" C1' I F 74 " pdb=" N9 I F 74 " pdb=" C4 I F 74 " ideal model delta sigma weight residual 106.08 124.85 -18.77 3.00e+00 1.11e-01 3.91e+01 ... (remaining 35123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13203 17.99 - 35.98: 1061 35.98 - 53.97: 347 53.97 - 71.96: 169 71.96 - 89.95: 174 Dihedral angle restraints: 14954 sinusoidal: 7202 harmonic: 7752 Sorted by residual: dihedral pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " pdb=" SG CYS C 677 " pdb=" CB CYS C 677 " ideal model delta sinusoidal sigma weight residual 93.00 163.12 -70.12 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " pdb=" SG CYS A 677 " pdb=" CB CYS A 677 " ideal model delta sinusoidal sigma weight residual 93.00 163.12 -70.12 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 649 " pdb=" SG CYS D 649 " pdb=" SG CYS D 677 " pdb=" CB CYS D 677 " ideal model delta sinusoidal sigma weight residual 93.00 163.08 -70.08 1 1.00e+01 1.00e-02 6.33e+01 ... (remaining 14951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2478 0.036 - 0.071: 999 0.071 - 0.107: 231 0.107 - 0.142: 83 0.142 - 0.178: 12 Chirality restraints: 3803 Sorted by residual: chirality pdb=" CB VAL B 82 " pdb=" CA VAL B 82 " pdb=" CG1 VAL B 82 " pdb=" CG2 VAL B 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB VAL D 82 " pdb=" CA VAL D 82 " pdb=" CG1 VAL D 82 " pdb=" CG2 VAL D 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CB VAL C 82 " pdb=" CA VAL C 82 " pdb=" CG1 VAL C 82 " pdb=" CG2 VAL C 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 3800 not shown) Planarity restraints: 3996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I F 39 " 0.219 2.00e-02 2.50e+03 6.12e-01 8.42e+03 pdb=" C2' I F 39 " -0.165 2.00e-02 2.50e+03 pdb=" C3' I F 39 " -0.604 2.00e-02 2.50e+03 pdb=" C4' I F 39 " 0.431 2.00e-02 2.50e+03 pdb=" C5' I F 39 " 0.075 2.00e-02 2.50e+03 pdb=" N9 I F 39 " -0.943 2.00e-02 2.50e+03 pdb=" O2' I F 39 " 1.003 2.00e-02 2.50e+03 pdb=" O3' I F 39 " -0.656 2.00e-02 2.50e+03 pdb=" O4' I F 39 " 0.641 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 73 " 0.200 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C2' I F 73 " -0.223 2.00e-02 2.50e+03 pdb=" C3' I F 73 " -0.586 2.00e-02 2.50e+03 pdb=" C4' I F 73 " 0.458 2.00e-02 2.50e+03 pdb=" C5' I F 73 " 0.034 2.00e-02 2.50e+03 pdb=" N9 I F 73 " -0.944 2.00e-02 2.50e+03 pdb=" O2' I F 73 " 0.904 2.00e-02 2.50e+03 pdb=" O3' I F 73 " -0.588 2.00e-02 2.50e+03 pdb=" O4' I F 73 " 0.745 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 4 " -0.201 2.00e-02 2.50e+03 5.99e-01 8.07e+03 pdb=" C2' I F 4 " 0.224 2.00e-02 2.50e+03 pdb=" C3' I F 4 " 0.589 2.00e-02 2.50e+03 pdb=" C4' I F 4 " -0.453 2.00e-02 2.50e+03 pdb=" C5' I F 4 " -0.034 2.00e-02 2.50e+03 pdb=" N9 I F 4 " 0.937 2.00e-02 2.50e+03 pdb=" O2' I F 4 " -0.903 2.00e-02 2.50e+03 pdb=" O3' I F 4 " 0.583 2.00e-02 2.50e+03 pdb=" O4' I F 4 " -0.743 2.00e-02 2.50e+03 ... (remaining 3993 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3566 2.76 - 3.30: 23180 3.30 - 3.83: 44173 3.83 - 4.37: 52701 4.37 - 4.90: 83771 Nonbonded interactions: 207391 Sorted by model distance: nonbonded pdb=" OG SER A 571 " pdb=" OP1 C E 57 " model vdw 2.227 2.440 nonbonded pdb=" O PHE C 84 " pdb=" O2' I F 39 " model vdw 2.228 3.040 nonbonded pdb=" ND1 HIS A 39 " pdb=" OP1 I F 7 " model vdw 2.249 2.520 nonbonded pdb=" ND1 HIS B 39 " pdb=" OP2 C E 42 " model vdw 2.265 2.520 nonbonded pdb=" N4 C E 11 " pdb=" O6 I F 70 " model vdw 2.344 2.520 ... (remaining 207386 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 'B' selection = chain 'C' selection = chain 'D' } 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: 5 Type Number sf(0) Gaussians P 158 5.49 5 S 68 5.16 5 C 15040 2.51 5 N 4144 2.21 5 O 5080 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.020 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: 0.020 Extract box with map and model: 29.310 Check model and map are aligned: 0.360 Process input model: 64.880 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.148 25336 Z= 0.780 Angle : 1.482 19.403 35128 Z= 0.547 Chirality : 0.042 0.178 3803 Planarity : 0.082 0.612 3996 Dihedral : 18.988 89.949 9858 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2628 helix: -1.64 (0.44), residues: 124 sheet: -1.69 (0.27), residues: 460 loop : -0.71 (0.15), residues: 2044 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.3705 time to fit residues: 292.3714 Evaluate side-chains 219 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.0770 chunk 203 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 156 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN B 597 ASN B 645 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 ASN D 597 ASN ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25336 Z= 0.191 Angle : 1.859 17.140 35128 Z= 1.157 Chirality : 0.041 0.212 3803 Planarity : 0.016 0.117 3996 Dihedral : 21.380 114.269 4658 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2628 helix: -1.50 (0.44), residues: 124 sheet: -1.91 (0.26), residues: 472 loop : -0.52 (0.15), residues: 2032 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 227 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 249 average time/residue: 0.3387 time to fit residues: 138.0154 Evaluate side-chains 190 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 2.673 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2112 time to fit residues: 8.8850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 241 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 410 HIS ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS A 678 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN B 597 ASN B 599 ASN ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN C 311 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 470 GLN ** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 312 HIS D 316 HIS D 359 HIS D 361 ASN D 365 ASN D 597 ASN D 599 ASN D 616 ASN ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 25336 Z= 0.450 Angle : 1.856 16.094 35128 Z= 1.129 Chirality : 0.048 0.203 3803 Planarity : 0.017 0.127 3996 Dihedral : 21.857 104.432 4658 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2628 helix: -1.93 (0.40), residues: 132 sheet: -1.64 (0.28), residues: 396 loop : -0.90 (0.14), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 24 residues processed: 255 average time/residue: 0.3578 time to fit residues: 148.8581 Evaluate side-chains 166 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2428 time to fit residues: 14.8360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 127 optimal weight: 0.0970 chunk 231 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 599 ASN B 645 ASN C 172 ASN C 229 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN D 361 ASN D 466 ASN D 494 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 25336 Z= 0.206 Angle : 1.761 15.547 35128 Z= 1.099 Chirality : 0.042 0.197 3803 Planarity : 0.016 0.119 3996 Dihedral : 21.834 98.127 4658 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2628 helix: -2.22 (0.38), residues: 156 sheet: -1.92 (0.26), residues: 432 loop : -0.71 (0.14), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 202 average time/residue: 0.3475 time to fit residues: 115.8359 Evaluate side-chains 150 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2630 time to fit residues: 8.1590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 221 optimal weight: 0.0370 chunk 179 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 overall best weight: 2.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 285 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS C 229 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN C 609 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 25336 Z= 0.353 Angle : 1.763 15.794 35128 Z= 1.096 Chirality : 0.045 0.192 3803 Planarity : 0.017 0.123 3996 Dihedral : 22.018 97.110 4658 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2628 helix: -2.33 (0.38), residues: 152 sheet: -1.84 (0.28), residues: 396 loop : -0.95 (0.14), residues: 2080 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 172 average time/residue: 0.3363 time to fit residues: 96.5506 Evaluate side-chains 147 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 3.079 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2201 time to fit residues: 9.1677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 25336 Z= 0.277 Angle : 1.725 15.731 35128 Z= 1.085 Chirality : 0.042 0.187 3803 Planarity : 0.016 0.120 3996 Dihedral : 22.114 93.766 4658 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 2628 helix: -2.32 (0.38), residues: 152 sheet: -2.08 (0.27), residues: 412 loop : -0.89 (0.14), residues: 2064 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 5 residues processed: 182 average time/residue: 0.3413 time to fit residues: 103.7120 Evaluate side-chains 143 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2406 time to fit residues: 5.6958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 144 optimal weight: 0.0570 chunk 258 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN C 39 HIS ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 25336 Z= 0.213 Angle : 1.698 15.718 35128 Z= 1.077 Chirality : 0.042 0.207 3803 Planarity : 0.016 0.119 3996 Dihedral : 22.209 95.632 4658 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2628 helix: -2.13 (0.39), residues: 152 sheet: -2.04 (0.27), residues: 428 loop : -0.80 (0.14), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 175 average time/residue: 0.3499 time to fit residues: 101.9956 Evaluate side-chains 147 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 2.744 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2286 time to fit residues: 5.8305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 154 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 203 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 597 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 25336 Z= 0.193 Angle : 1.678 15.582 35128 Z= 1.072 Chirality : 0.041 0.206 3803 Planarity : 0.016 0.118 3996 Dihedral : 22.306 97.694 4658 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2628 helix: -2.12 (0.40), residues: 152 sheet: -2.03 (0.26), residues: 428 loop : -0.78 (0.14), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 171 average time/residue: 0.3424 time to fit residues: 97.3254 Evaluate side-chains 143 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 2.872 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2269 time to fit residues: 5.4967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 0.4980 chunk 225 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 25336 Z= 0.205 Angle : 1.675 15.477 35128 Z= 1.071 Chirality : 0.042 0.199 3803 Planarity : 0.016 0.119 3996 Dihedral : 22.390 97.596 4658 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2628 helix: -2.17 (0.39), residues: 156 sheet: -2.03 (0.27), residues: 428 loop : -0.77 (0.15), residues: 2044 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 148 average time/residue: 0.3332 time to fit residues: 84.7775 Evaluate side-chains 145 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 2.865 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2237 time to fit residues: 5.7334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 245 optimal weight: 0.0170 chunk 212 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 164 optimal weight: 0.0040 chunk 130 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 overall best weight: 1.3232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 25336 Z= 0.206 Angle : 1.673 15.963 35128 Z= 1.069 Chirality : 0.042 0.200 3803 Planarity : 0.016 0.119 3996 Dihedral : 22.445 97.742 4658 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2628 helix: -2.39 (0.37), residues: 156 sheet: -2.03 (0.27), residues: 428 loop : -0.80 (0.15), residues: 2044 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3322 time to fit residues: 80.8462 Evaluate side-chains 137 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 196 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 285 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN C 609 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.081830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.070106 restraints weight = 101784.803| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.17 r_work: 0.3452 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 25336 Z= 0.358 Angle : 1.715 15.504 35128 Z= 1.081 Chirality : 0.045 0.217 3803 Planarity : 0.017 0.123 3996 Dihedral : 22.423 96.982 4658 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2628 helix: -2.44 (0.35), residues: 176 sheet: -2.17 (0.27), residues: 380 loop : -1.15 (0.14), residues: 2072 =============================================================================== Job complete usr+sys time: 4606.20 seconds wall clock time: 86 minutes 34.07 seconds (5194.07 seconds total)