Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 17:26:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/07_2023/7k23_22641.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/07_2023/7k23_22641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/07_2023/7k23_22641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/07_2023/7k23_22641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/07_2023/7k23_22641.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k23_22641/07_2023/7k23_22641.pdb" } resolution = 3.3 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 13914 2.51 5 N 3662 2.21 5 O 4228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L2 ARG 24": "NH1" <-> "NH2" Residue "L2 ARG 61": "NH1" <-> "NH2" Residue "L2 GLU 81": "OE1" <-> "OE2" Residue "H2 ARG 62": "NH1" <-> "NH2" Residue "H2 ARG 67": "NH1" <-> "NH2" Residue "H2 ARG 77": "NH1" <-> "NH2" Residue "H2 ARG 95": "NH1" <-> "NH2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "L3 ARG 24": "NH1" <-> "NH2" Residue "L3 ARG 61": "NH1" <-> "NH2" Residue "L3 GLU 81": "OE1" <-> "OE2" Residue "H3 ARG 62": "NH1" <-> "NH2" Residue "H3 ARG 67": "NH1" <-> "NH2" Residue "H3 ARG 77": "NH1" <-> "NH2" Residue "H3 ARG 95": "NH1" <-> "NH2" Residue "L4 ARG 24": "NH1" <-> "NH2" Residue "L4 ARG 61": "NH1" <-> "NH2" Residue "L4 GLU 81": "OE1" <-> "OE2" Residue "H4 ARG 62": "NH1" <-> "NH2" Residue "H4 ARG 67": "NH1" <-> "NH2" Residue "H4 ARG 77": "NH1" <-> "NH2" Residue "H4 ARG 95": "NH1" <-> "NH2" Residue "L5 ARG 24": "NH1" <-> "NH2" Residue "L5 ARG 61": "NH1" <-> "NH2" Residue "L5 GLU 81": "OE1" <-> "OE2" Residue "H5 ARG 62": "NH1" <-> "NH2" Residue "H5 ARG 67": "NH1" <-> "NH2" Residue "H5 ARG 77": "NH1" <-> "NH2" Residue "H5 ARG 95": "NH1" <-> "NH2" Residue "L6 ARG 24": "NH1" <-> "NH2" Residue "L6 ARG 61": "NH1" <-> "NH2" Residue "L6 GLU 81": "OE1" <-> "OE2" Residue "H6 ARG 62": "NH1" <-> "NH2" Residue "H6 ARG 67": "NH1" <-> "NH2" Residue "H6 ARG 77": "NH1" <-> "NH2" Residue "H6 ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 21923 Number of models: 1 Model: "" Number of chains: 15 Chain: "L2" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H2" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "A" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2854 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 31, 'TRANS': 334} Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 31, 'TRANS': 335} Chain: "C" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2789 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 30, 'TRANS': 326} Chain: "D" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2650 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 27, 'TRANS': 312} Chain: "E" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 31, 'TRANS': 334} Chain: "L3" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H3" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "L4" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H4" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "L5" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H5" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "L6" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H6" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Time building chain proxies: 10.47, per 1000 atoms: 0.48 Number of scatterers: 21923 At special positions: 0 Unit cell: (167.2, 163.9, 132, 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 119 16.00 O 4228 8.00 N 3662 7.00 C 13914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYSL2 23 " - pdb=" SG CYSL2 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH2 18 " - pdb=" SG CYSH2 91 " distance=2.02 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS E 3 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS E 98 " distance=2.02 Simple disulfide: pdb=" SG CYSL3 23 " - pdb=" SG CYSL3 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH3 18 " - pdb=" SG CYSH3 91 " distance=2.02 Simple disulfide: pdb=" SG CYSL4 23 " - pdb=" SG CYSL4 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH4 18 " - pdb=" SG CYSH4 91 " distance=2.02 Simple disulfide: pdb=" SG CYSL5 23 " - pdb=" SG CYSL5 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH5 18 " - pdb=" SG CYSH5 91 " distance=2.02 Simple disulfide: pdb=" SG CYSL6 23 " - pdb=" SG CYSL6 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH6 18 " - pdb=" SG CYSH6 91 " distance=2.02 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: 8.00 Conformation dependent library (CDL) restraints added in 3.3 seconds 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 50 sheets defined 9.7% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'L2' and resid 49 through 52 removed outlier: 3.658A pdb=" N SERL2 52 " --> pdb=" O TYRL2 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L2' and resid 49 through 52' Processing helix chain 'L2' and resid 79 through 83 removed outlier: 3.542A pdb=" N LEUL2 83 " --> pdb=" O THRL2 80 " (cutoff:3.500A) Processing helix chain 'H2' and resid 24 through 28 removed outlier: 3.531A pdb=" N SERH2 27 " --> pdb=" O THRH2 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYRH2 28 " --> pdb=" O PHEH2 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 24 through 28' Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 326 through 330 removed outlier: 4.085A pdb=" N ASN A 329 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 330 " --> pdb=" O GLY A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 304 through 315 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.952A pdb=" N LEU C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 3.611A pdb=" N ARG C 356 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.552A pdb=" N VAL D 191 " --> pdb=" O LYS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 186 through 191 removed outlier: 3.720A pdb=" N VAL E 191 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 317 Processing helix chain 'L3' and resid 49 through 52 removed outlier: 3.657A pdb=" N SERL3 52 " --> pdb=" O TYRL3 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L3' and resid 49 through 52' Processing helix chain 'L3' and resid 79 through 83 removed outlier: 3.541A pdb=" N LEUL3 83 " --> pdb=" O THRL3 80 " (cutoff:3.500A) Processing helix chain 'H3' and resid 24 through 28 removed outlier: 3.531A pdb=" N SERH3 27 " --> pdb=" O THRH3 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYRH3 28 " --> pdb=" O PHEH3 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H3' and resid 24 through 28' Processing helix chain 'L4' and resid 49 through 52 removed outlier: 3.657A pdb=" N SERL4 52 " --> pdb=" O TYRL4 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L4' and resid 49 through 52' Processing helix chain 'L4' and resid 79 through 83 removed outlier: 3.541A pdb=" N LEUL4 83 " --> pdb=" O THRL4 80 " (cutoff:3.500A) Processing helix chain 'H4' and resid 24 through 28 removed outlier: 3.530A pdb=" N SERH4 27 " --> pdb=" O THRH4 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYRH4 28 " --> pdb=" O PHEH4 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H4' and resid 24 through 28' Processing helix chain 'L5' and resid 49 through 52 removed outlier: 3.657A pdb=" N SERL5 52 " --> pdb=" O TYRL5 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L5' and resid 49 through 52' Processing helix chain 'L5' and resid 79 through 83 removed outlier: 3.541A pdb=" N LEUL5 83 " --> pdb=" O THRL5 80 " (cutoff:3.500A) Processing helix chain 'H5' and resid 24 through 28 removed outlier: 3.530A pdb=" N SERH5 27 " --> pdb=" O THRH5 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYRH5 28 " --> pdb=" O PHEH5 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H5' and resid 24 through 28' Processing helix chain 'L6' and resid 49 through 52 removed outlier: 3.658A pdb=" N SERL6 52 " --> pdb=" O TYRL6 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L6' and resid 49 through 52' Processing helix chain 'L6' and resid 79 through 83 removed outlier: 3.542A pdb=" N LEUL6 83 " --> pdb=" O THRL6 80 " (cutoff:3.500A) Processing helix chain 'H6' and resid 24 through 28 removed outlier: 3.530A pdb=" N SERH6 27 " --> pdb=" O THRH6 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYRH6 28 " --> pdb=" O PHEH6 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H6' and resid 24 through 28' Processing sheet with id=AA1, first strand: chain 'L2' and resid 4 through 6 removed outlier: 5.789A pdb=" N THRL2 69 " --> pdb=" O ALAL2 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L2' and resid 45 through 48 removed outlier: 6.470A pdb=" N TRPL2 35 " --> pdb=" O VALL2 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H2' and resid 18 through 19 removed outlier: 4.057A pdb=" N THRH2 73 " --> pdb=" O ASPH2 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H2' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH2 40 " --> pdb=" O VALH2 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH2 36 " --> pdb=" O GLYH2 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH2 32 " --> pdb=" O VALH2 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYRH2 46 " --> pdb=" O METH2 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METH2 30 " --> pdb=" O TYRH2 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILEH2 33 " --> pdb=" O TYRH2 90 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYRH2 107 " --> pdb=" O ARGH2 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 37 removed outlier: 6.510A pdb=" N TYR A 289 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 111 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS A 291 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 109 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A 293 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 88 removed outlier: 6.231A pdb=" N ARG A 284 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP A 272 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS A 282 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.241A pdb=" N ILE A 137 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 197 through 199 Processing sheet with id=AB1, first strand: chain 'A' and resid 236 through 240 Processing sheet with id=AB2, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.690A pdb=" N ARG B 284 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP B 272 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS B 282 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.519A pdb=" N TYR B 289 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR B 111 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS B 291 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 109 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 293 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.519A pdb=" N TYR B 289 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR B 111 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS B 291 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 109 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 293 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.207A pdb=" N ILE B 137 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 197 through 198 Processing sheet with id=AB8, first strand: chain 'B' and resid 236 through 240 Processing sheet with id=AB9, first strand: chain 'B' and resid 236 through 240 removed outlier: 6.335A pdb=" N ARG C 284 " --> pdb=" O MET C 270 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP C 272 " --> pdb=" O HIS C 282 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS C 282 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 355 Processing sheet with id=AC2, first strand: chain 'C' and resid 30 through 37 removed outlier: 6.493A pdb=" N TYR C 289 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR C 111 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS C 291 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL C 109 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR C 293 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 128 through 130 removed outlier: 5.983A pdb=" N ILE C 137 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AC5, first strand: chain 'C' and resid 236 through 240 Processing sheet with id=AC6, first strand: chain 'C' and resid 236 through 240 removed outlier: 6.452A pdb=" N ARG D 284 " --> pdb=" O MET D 270 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 30 through 37 removed outlier: 6.499A pdb=" N TYR D 289 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 111 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS D 291 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 109 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR D 293 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 30 through 37 removed outlier: 6.499A pdb=" N TYR D 289 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 111 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS D 291 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 109 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR D 293 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 128 through 130 removed outlier: 6.271A pdb=" N ILE D 137 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 197 through 199 Processing sheet with id=AD2, first strand: chain 'D' and resid 236 through 240 Processing sheet with id=AD3, first strand: chain 'D' and resid 236 through 240 removed outlier: 4.494A pdb=" N GLY E 271 " --> pdb=" O ARG E 284 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 31 through 37 removed outlier: 6.492A pdb=" N TYR E 289 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR E 111 " --> pdb=" O TYR E 289 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS E 291 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL E 109 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR E 293 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 128 through 130 removed outlier: 5.939A pdb=" N ILE E 137 " --> pdb=" O PRO E 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 197 through 199 Processing sheet with id=AD7, first strand: chain 'E' and resid 351 through 354 removed outlier: 4.003A pdb=" N THR E 351 " --> pdb=" O THR E 362 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L3' and resid 4 through 6 removed outlier: 5.790A pdb=" N THRL3 69 " --> pdb=" O ALAL3 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L3' and resid 45 through 48 removed outlier: 6.471A pdb=" N TRPL3 35 " --> pdb=" O VALL3 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H3' and resid 18 through 19 removed outlier: 4.058A pdb=" N THRH3 73 " --> pdb=" O ASPH3 68 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H3' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH3 40 " --> pdb=" O VALH3 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH3 36 " --> pdb=" O GLYH3 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH3 32 " --> pdb=" O VALH3 44 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYRH3 46 " --> pdb=" O METH3 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METH3 30 " --> pdb=" O TYRH3 46 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILEH3 33 " --> pdb=" O TYRH3 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYRH3 107 " --> pdb=" O ARGH3 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L4' and resid 4 through 6 removed outlier: 5.789A pdb=" N THRL4 69 " --> pdb=" O ALAL4 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L4' and resid 45 through 48 removed outlier: 6.471A pdb=" N TRPL4 35 " --> pdb=" O VALL4 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H4' and resid 18 through 19 removed outlier: 4.059A pdb=" N THRH4 73 " --> pdb=" O ASPH4 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H4' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH4 40 " --> pdb=" O VALH4 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH4 36 " --> pdb=" O GLYH4 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH4 32 " --> pdb=" O VALH4 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYRH4 46 " --> pdb=" O METH4 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N METH4 30 " --> pdb=" O TYRH4 46 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILEH4 33 " --> pdb=" O TYRH4 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYRH4 107 " --> pdb=" O ARGH4 93 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L5' and resid 4 through 6 removed outlier: 5.790A pdb=" N THRL5 69 " --> pdb=" O ALAL5 25 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L5' and resid 45 through 48 removed outlier: 6.471A pdb=" N TRPL5 35 " --> pdb=" O VALL5 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H5' and resid 18 through 19 removed outlier: 4.057A pdb=" N THRH5 73 " --> pdb=" O ASPH5 68 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H5' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH5 40 " --> pdb=" O VALH5 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH5 36 " --> pdb=" O GLYH5 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH5 32 " --> pdb=" O VALH5 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYRH5 46 " --> pdb=" O METH5 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METH5 30 " --> pdb=" O TYRH5 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILEH5 33 " --> pdb=" O TYRH5 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYRH5 107 " --> pdb=" O ARGH5 93 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L6' and resid 4 through 6 removed outlier: 5.790A pdb=" N THRL6 69 " --> pdb=" O ALAL6 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L6' and resid 45 through 48 removed outlier: 6.471A pdb=" N TRPL6 35 " --> pdb=" O VALL6 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H6' and resid 18 through 19 removed outlier: 4.058A pdb=" N THRH6 73 " --> pdb=" O ASPH6 68 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H6' and resid 53 through 55 removed outlier: 3.681A pdb=" N GLYH6 40 " --> pdb=" O VALH6 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALH6 36 " --> pdb=" O GLYH6 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRPH6 32 " --> pdb=" O VALH6 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYRH6 46 " --> pdb=" O METH6 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METH6 30 " --> pdb=" O TYRH6 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILEH6 33 " --> pdb=" O TYRH6 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYRH6 107 " --> pdb=" O ARGH6 93 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1674 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: 7.03 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3633 1.31 - 1.44: 6194 1.44 - 1.57: 12464 1.57 - 1.70: 0 1.70 - 1.83: 198 Bond restraints: 22489 Sorted by residual: bond pdb=" C VAL E 274 " pdb=" O VAL E 274 " ideal model delta sigma weight residual 1.237 1.185 0.053 1.08e-02 8.57e+03 2.38e+01 bond pdb=" CA VAL E 274 " pdb=" CB VAL E 274 " ideal model delta sigma weight residual 1.535 1.487 0.048 1.24e-02 6.50e+03 1.53e+01 bond pdb=" C LEU A 37 " pdb=" N ASN A 38 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.25e+00 bond pdb=" C SER D 73 " pdb=" N PRO D 74 " ideal model delta sigma weight residual 1.337 1.317 0.020 9.80e-03 1.04e+04 3.99e+00 bond pdb=" C LEU D 50 " pdb=" N THR D 51 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.40e-02 5.10e+03 3.25e+00 ... (remaining 22484 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.89: 684 105.89 - 112.95: 12001 112.95 - 120.02: 7437 120.02 - 127.09: 10182 127.09 - 134.15: 329 Bond angle restraints: 30633 Sorted by residual: angle pdb=" N VAL D 320 " pdb=" CA VAL D 320 " pdb=" C VAL D 320 " ideal model delta sigma weight residual 109.29 119.84 -10.55 1.42e+00 4.96e-01 5.52e+01 angle pdb=" N VAL E 274 " pdb=" CA VAL E 274 " pdb=" C VAL E 274 " ideal model delta sigma weight residual 107.37 118.16 -10.79 1.48e+00 4.57e-01 5.32e+01 angle pdb=" N GLN C 321 " pdb=" CA GLN C 321 " pdb=" C GLN C 321 " ideal model delta sigma weight residual 111.36 118.80 -7.44 1.09e+00 8.42e-01 4.66e+01 angle pdb=" N GLY B 259 " pdb=" CA GLY B 259 " pdb=" C GLY B 259 " ideal model delta sigma weight residual 113.18 100.62 12.56 2.37e+00 1.78e-01 2.81e+01 angle pdb=" C ARG D 5 " pdb=" N PRO D 6 " pdb=" CA PRO D 6 " ideal model delta sigma weight residual 119.85 124.67 -4.82 1.01e+00 9.80e-01 2.28e+01 ... (remaining 30628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11522 17.98 - 35.96: 1423 35.96 - 53.94: 351 53.94 - 71.91: 72 71.91 - 89.89: 33 Dihedral angle restraints: 13401 sinusoidal: 5369 harmonic: 8032 Sorted by residual: dihedral pdb=" CB CYSH4 18 " pdb=" SG CYSH4 18 " pdb=" SG CYSH4 91 " pdb=" CB CYSH4 91 " ideal model delta sinusoidal sigma weight residual 93.00 140.55 -47.55 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYSH5 18 " pdb=" SG CYSH5 18 " pdb=" SG CYSH5 91 " pdb=" CB CYSH5 91 " ideal model delta sinusoidal sigma weight residual 93.00 140.52 -47.52 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYSH6 18 " pdb=" SG CYSH6 18 " pdb=" SG CYSH6 91 " pdb=" CB CYSH6 91 " ideal model delta sinusoidal sigma weight residual 93.00 140.52 -47.52 1 1.00e+01 1.00e-02 3.12e+01 ... (remaining 13398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2574 0.053 - 0.105: 656 0.105 - 0.158: 121 0.158 - 0.210: 9 0.210 - 0.263: 6 Chirality restraints: 3366 Sorted by residual: chirality pdb=" CA GLN E 55 " pdb=" N GLN E 55 " pdb=" C GLN E 55 " pdb=" CB GLN E 55 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLN C 55 " pdb=" N GLN C 55 " pdb=" C GLN C 55 " pdb=" CB GLN C 55 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA GLN D 55 " pdb=" N GLN D 55 " pdb=" C GLN D 55 " pdb=" CB GLN D 55 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3363 not shown) Planarity restraints: 3948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 73 " 0.050 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO E 74 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 73 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO D 74 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 355 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C ASP B 355 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP B 355 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG B 356 " 0.016 2.00e-02 2.50e+03 ... (remaining 3945 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 39 2.28 - 2.93: 9782 2.93 - 3.59: 28657 3.59 - 4.24: 50456 4.24 - 4.90: 86024 Nonbonded interactions: 174958 Sorted by model distance: nonbonded pdb=" CD2 LEU E 50 " pdb=" CB GLN E 55 " model vdw 1.620 3.860 nonbonded pdb=" NE1 TRP E 272 " pdb=" CZ2 TRP E 283 " model vdw 1.766 3.420 nonbonded pdb=" CD2 LEU E 50 " pdb=" CG GLN E 55 " model vdw 1.889 3.860 nonbonded pdb=" CG2 THRH2 98 " pdb=" ND2 ASN C 277 " model vdw 1.911 3.540 nonbonded pdb=" CE MET C 103 " pdb=" O CYS C 257 " model vdw 2.062 3.460 ... (remaining 174953 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' and resid 2 through 340) selection = (chain 'B' and resid 2 through 340) selection = (chain 'C' and resid 2 through 340) selection = (chain 'D' and resid 2 through 340) selection = (chain 'E' and resid 2 through 340) } ncs_group { reference = chain 'H2' selection = chain 'H3' selection = chain 'H4' selection = chain 'H5' selection = chain 'H6' } ncs_group { reference = chain 'L2' selection = chain 'L3' selection = chain 'L4' selection = chain 'L5' selection = chain 'L6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 8.080 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 53.960 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 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 : 0.007 0.076 22489 Z= 0.436 Angle : 0.808 12.558 30633 Z= 0.457 Chirality : 0.049 0.263 3366 Planarity : 0.005 0.077 3948 Dihedral : 17.183 89.893 8234 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.27 % Favored : 90.51 % Rotamer Outliers : 5.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -3.86 (0.13), residues: 2751 helix: -3.24 (0.32), residues: 141 sheet: -1.43 (0.18), residues: 729 loop : -3.22 (0.11), residues: 1881 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 406 time to evaluate : 2.556 Fit side-chains revert: symmetry clash outliers start: 132 outliers final: 70 residues processed: 509 average time/residue: 0.3151 time to fit residues: 252.6116 Evaluate side-chains 410 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 340 time to evaluate : 2.514 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.2010 time to fit residues: 29.5072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L2 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 37 GLN H2 69 ASN A 88 GLN A 126 ASN A 190 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 126 ASN B 147 HIS B 190 GLN B 282 HIS B 314 ASN B 321 GLN B 323 GLN B 331 GLN C 38 ASN C 55 GLN C 126 ASN C 147 HIS C 277 ASN C 282 HIS C 323 GLN C 331 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 HIS ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN E 88 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN E 126 ASN E 145 GLN E 147 HIS E 190 GLN E 282 HIS E 319 GLN E 323 GLN L3 22 ASN L3 37 GLN H3 69 ASN ** L4 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 32 ASN L4 37 GLN L4 92 ASN H4 69 ASN L5 37 GLN ** H5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 22 ASN L6 37 GLN L6 38 GLN H6 35 GLN H6 69 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 22489 Z= 0.292 Angle : 0.671 11.131 30633 Z= 0.346 Chirality : 0.047 0.215 3366 Planarity : 0.005 0.065 3948 Dihedral : 5.861 26.981 3028 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.56 % Favored : 90.33 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -3.17 (0.14), residues: 2751 helix: -2.56 (0.38), residues: 141 sheet: -0.94 (0.18), residues: 762 loop : -2.78 (0.12), residues: 1848 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 367 time to evaluate : 2.517 Fit side-chains outliers start: 90 outliers final: 49 residues processed: 432 average time/residue: 0.3249 time to fit residues: 225.6618 Evaluate side-chains 390 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 341 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2327 time to fit residues: 23.7577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 40.0000 chunk 165 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L2 22 ASN H2 69 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 88 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 22 ASN L5 38 GLN H5 35 GLN H5 69 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 22489 Z= 0.253 Angle : 0.629 12.635 30633 Z= 0.321 Chirality : 0.046 0.204 3366 Planarity : 0.005 0.054 3948 Dihedral : 5.501 28.538 3028 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.98 % Favored : 90.88 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.69 (0.14), residues: 2751 helix: -2.10 (0.42), residues: 135 sheet: -0.60 (0.18), residues: 770 loop : -2.46 (0.13), residues: 1846 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 349 time to evaluate : 2.520 Fit side-chains outliers start: 82 outliers final: 42 residues processed: 401 average time/residue: 0.2859 time to fit residues: 187.6016 Evaluate side-chains 370 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 328 time to evaluate : 2.469 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2008 time to fit residues: 18.9722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 53 ASN ** H4 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 22489 Z= 0.321 Angle : 0.665 11.811 30633 Z= 0.339 Chirality : 0.047 0.205 3366 Planarity : 0.005 0.054 3948 Dihedral : 5.631 28.147 3028 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.56 % Favored : 90.29 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.43 (0.15), residues: 2751 helix: -1.87 (0.45), residues: 129 sheet: -0.38 (0.18), residues: 772 loop : -2.30 (0.13), residues: 1850 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 357 time to evaluate : 2.440 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 32 residues processed: 406 average time/residue: 0.2932 time to fit residues: 194.4935 Evaluate side-chains 378 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 346 time to evaluate : 2.614 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2196 time to fit residues: 16.9215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 30.0000 chunk 146 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 192 optimal weight: 0.0870 chunk 106 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 231 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 38 GLN H3 35 GLN L4 38 GLN L4 92 ASN ** H4 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H4 35 GLN L5 22 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 22489 Z= 0.253 Angle : 0.620 12.386 30633 Z= 0.315 Chirality : 0.045 0.235 3366 Planarity : 0.004 0.049 3948 Dihedral : 5.415 29.019 3028 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.83 % Favored : 91.06 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.16 (0.15), residues: 2751 helix: -1.54 (0.47), residues: 123 sheet: -0.16 (0.19), residues: 766 loop : -2.13 (0.13), residues: 1862 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 342 time to evaluate : 2.550 Fit side-chains outliers start: 52 outliers final: 28 residues processed: 373 average time/residue: 0.2927 time to fit residues: 179.7064 Evaluate side-chains 362 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 334 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2020 time to fit residues: 14.0295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 258 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN D 321 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN H4 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 22489 Z= 0.342 Angle : 0.677 12.292 30633 Z= 0.342 Chirality : 0.047 0.221 3366 Planarity : 0.005 0.049 3948 Dihedral : 5.611 28.018 3028 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.92 % Favored : 89.93 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.08 (0.15), residues: 2751 helix: -1.46 (0.48), residues: 122 sheet: -0.09 (0.19), residues: 757 loop : -2.08 (0.13), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 333 time to evaluate : 2.556 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 34 residues processed: 375 average time/residue: 0.3020 time to fit residues: 188.4452 Evaluate side-chains 365 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 331 time to evaluate : 2.479 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2050 time to fit residues: 16.6550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 257 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 22489 Z= 0.311 Angle : 0.657 13.027 30633 Z= 0.332 Chirality : 0.047 0.248 3366 Planarity : 0.005 0.050 3948 Dihedral : 5.542 28.349 3028 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.38 % Favored : 90.48 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.06 (0.15), residues: 2751 helix: -1.42 (0.48), residues: 123 sheet: -0.03 (0.19), residues: 735 loop : -2.07 (0.13), residues: 1893 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 341 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 370 average time/residue: 0.2963 time to fit residues: 178.2930 Evaluate side-chains 348 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 329 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2305 time to fit residues: 11.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 163 optimal weight: 0.2980 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 202 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 102 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN L6 32 ASN L6 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 22489 Z= 0.154 Angle : 0.567 12.693 30633 Z= 0.288 Chirality : 0.043 0.222 3366 Planarity : 0.004 0.052 3948 Dihedral : 5.011 30.463 3028 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.86 (0.15), residues: 2751 helix: -1.20 (0.50), residues: 123 sheet: 0.00 (0.19), residues: 742 loop : -1.89 (0.13), residues: 1886 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 357 time to evaluate : 2.668 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 365 average time/residue: 0.2985 time to fit residues: 177.7070 Evaluate side-chains 339 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 330 time to evaluate : 2.530 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2821 time to fit residues: 7.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 6.9990 chunk 246 optimal weight: 0.0070 chunk 224 optimal weight: 4.9990 chunk 239 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN E 88 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.086 22489 Z= 0.438 Angle : 0.726 11.912 30633 Z= 0.368 Chirality : 0.049 0.252 3366 Planarity : 0.005 0.056 3948 Dihedral : 5.689 28.072 3028 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.18 % Favored : 89.64 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.15), residues: 2751 helix: -1.67 (0.47), residues: 123 sheet: -0.09 (0.19), residues: 760 loop : -2.01 (0.13), residues: 1868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 325 time to evaluate : 2.541 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 338 average time/residue: 0.2886 time to fit residues: 159.9375 Evaluate side-chains 331 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 318 time to evaluate : 2.325 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1875 time to fit residues: 7.8986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 22489 Z= 0.245 Angle : 0.626 13.175 30633 Z= 0.318 Chirality : 0.046 0.295 3366 Planarity : 0.005 0.056 3948 Dihedral : 5.369 29.378 3028 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.51 % Favored : 91.38 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.89 (0.15), residues: 2751 helix: -1.61 (0.47), residues: 123 sheet: 0.08 (0.19), residues: 731 loop : -1.91 (0.13), residues: 1897 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 325 time to evaluate : 2.470 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 330 average time/residue: 0.2915 time to fit residues: 158.1614 Evaluate side-chains 323 residues out of total 2446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 318 time to evaluate : 2.505 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2342 time to fit residues: 5.8121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 9.9990 chunk 225 optimal weight: 0.0870 chunk 64 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.172326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.136442 restraints weight = 23707.355| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.41 r_work: 0.3103 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 22489 Z= 0.218 Angle : 0.607 13.124 30633 Z= 0.307 Chirality : 0.045 0.305 3366 Planarity : 0.005 0.055 3948 Dihedral : 5.185 29.979 3028 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.94 % Favored : 90.99 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.79 (0.15), residues: 2751 helix: -1.58 (0.48), residues: 122 sheet: 0.14 (0.20), residues: 720 loop : -1.83 (0.13), residues: 1909 =============================================================================== Job complete usr+sys time: 4799.76 seconds wall clock time: 87 minutes 55.01 seconds (5275.01 seconds total)