Starting phenix.real_space_refine (version: dev) on Thu Feb 23 21:36:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/02_2023/6nqa_0480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/02_2023/6nqa_0480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/02_2023/6nqa_0480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/02_2023/6nqa_0480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/02_2023/6nqa_0480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/02_2023/6nqa_0480_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 64": "OD1" <-> "OD2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 161": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K ASP 222": "OD1" <-> "OD2" Residue "K PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "K GLU 230": "OE1" <-> "OE2" Residue "K PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 262": "OE1" <-> "OE2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "K TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ASP 58": "OD1" <-> "OD2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L ARG 74": "NH1" <-> "NH2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15322 Number of models: 1 Model: "" Number of chains: 13 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2673 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 17, 'TRANS': 310} Chain: "L" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "C" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 Time building chain proxies: 8.78, per 1000 atoms: 0.57 Number of scatterers: 15322 At special positions: 0 Unit cell: (125.552, 126.616, 119.168, 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 24 16.00 P 292 15.00 O 3434 8.00 N 2825 7.00 C 8747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 3 sheets defined 49.7% alpha, 2.9% beta 135 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.707A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 74 removed outlier: 4.806A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.528A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 removed outlier: 3.761A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 17 through 21' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.890A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.566A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 80 removed outlier: 3.790A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 101 removed outlier: 3.770A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 122 removed outlier: 4.384A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 47 Processing helix chain 'K' and resid 49 through 56 Processing helix chain 'K' and resid 68 through 89 removed outlier: 3.663A pdb=" N ARG K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'K' and resid 122 through 126 removed outlier: 3.553A pdb=" N LEU K 125 " --> pdb=" O PRO K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 150 Processing helix chain 'K' and resid 168 through 176 Processing helix chain 'K' and resid 189 through 208 removed outlier: 4.003A pdb=" N TYR K 194 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 232 removed outlier: 3.668A pdb=" N ARG K 229 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU K 230 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 256 removed outlier: 3.941A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 290 Processing helix chain 'K' and resid 320 through 328 Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 56 through 59 Processing helix chain 'E' and resid 47 through 56 removed outlier: 4.575A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.619A pdb=" N ALA E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 97 Processing helix chain 'E' and resid 100 through 114 removed outlier: 4.023A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 131 removed outlier: 3.861A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 4.484A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.668A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 114 removed outlier: 3.935A pdb=" N TYR A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 101 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A 113 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 removed outlier: 4.462A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.612A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.646A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 122 removed outlier: 4.255A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.576A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.999A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.741A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.666A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.762A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.789A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL K 237 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU K 162 " --> pdb=" O VAL K 237 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE K 239 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG K 265 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 291 through 294 Processing sheet with id= C, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.541A pdb=" N ARG L 42 " --> pdb=" O VAL L 70 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3019 1.33 - 1.45: 4917 1.45 - 1.57: 7648 1.57 - 1.69: 582 1.69 - 1.81: 42 Bond restraints: 16208 Sorted by residual: bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.500 -0.078 3.00e-02 1.11e+03 6.74e+00 bond pdb=" C2 SAM K 500 " pdb=" N3 SAM K 500 " ideal model delta sigma weight residual 1.322 1.372 -0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" C8 SAM K 500 " pdb=" N7 SAM K 500 " ideal model delta sigma weight residual 1.298 1.348 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C2 SAM K 500 " pdb=" N1 SAM K 500 " ideal model delta sigma weight residual 1.329 1.377 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" C3' DG J 136 " pdb=" O3' DG J 136 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.09e+00 ... (remaining 16203 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.53: 1503 105.53 - 112.65: 8816 112.65 - 119.77: 5723 119.77 - 126.89: 6302 126.89 - 134.01: 815 Bond angle restraints: 23159 Sorted by residual: angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 126.26 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" N ALA C 47 " pdb=" CA ALA C 47 " pdb=" C ALA C 47 " ideal model delta sigma weight residual 109.81 117.39 -7.58 2.21e+00 2.05e-01 1.18e+01 angle pdb=" C3' DG J 136 " pdb=" O3' DG J 136 " pdb=" P DG J 137 " ideal model delta sigma weight residual 120.20 125.31 -5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N LEU A 65 " pdb=" CA LEU A 65 " pdb=" C LEU A 65 " ideal model delta sigma weight residual 109.81 117.15 -7.34 2.21e+00 2.05e-01 1.10e+01 angle pdb=" C ASN K 57 " pdb=" N TYR K 58 " pdb=" CA TYR K 58 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 ... (remaining 23154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 7289 33.91 - 67.82: 1425 67.82 - 101.73: 21 101.73 - 135.64: 1 135.64 - 169.55: 3 Dihedral angle restraints: 8739 sinusoidal: 5343 harmonic: 3396 Sorted by residual: dihedral pdb=" CA ASP K 62 " pdb=" C ASP K 62 " pdb=" N TYR K 63 " pdb=" CA TYR K 63 " ideal model delta harmonic sigma weight residual 180.00 -148.04 -31.96 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA TYR K 312 " pdb=" C TYR K 312 " pdb=" N TYR K 313 " pdb=" CA TYR K 313 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLN E 85 " pdb=" C GLN E 85 " pdb=" N SER E 86 " pdb=" CA SER E 86 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 8736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2194 0.063 - 0.127: 369 0.127 - 0.190: 49 0.190 - 0.253: 9 0.253 - 0.317: 1 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CB ILE H 89 " pdb=" CA ILE H 89 " pdb=" CG1 ILE H 89 " pdb=" CG2 ILE H 89 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE K 279 " pdb=" CA ILE K 279 " pdb=" CG1 ILE K 279 " pdb=" CG2 ILE K 279 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TYR K 312 " pdb=" N TYR K 312 " pdb=" C TYR K 312 " pdb=" CB TYR K 312 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2619 not shown) Planarity restraints: 1924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO A 66 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 190 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO K 191 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO K 191 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 191 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 132 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO K 133 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO K 133 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 133 " -0.034 5.00e-02 4.00e+02 ... (remaining 1921 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3631 2.81 - 3.33: 12644 3.33 - 3.85: 28042 3.85 - 4.38: 30419 4.38 - 4.90: 44435 Nonbonded interactions: 119171 Sorted by model distance: nonbonded pdb=" O SER D 91 " pdb=" OG SER D 91 " model vdw 2.283 2.440 nonbonded pdb=" O SER H 91 " pdb=" OG SER H 91 " model vdw 2.291 2.440 nonbonded pdb=" OP1 DG I 122 " pdb=" OH TYR H 40 " model vdw 2.299 2.440 nonbonded pdb=" O SER D 123 " pdb=" OG SER D 123 " model vdw 2.317 2.440 nonbonded pdb=" OD1 ASP K 199 " pdb=" OH TYR K 216 " model vdw 2.342 2.440 ... (remaining 119166 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 38 through 133) selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 124) } 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 292 5.49 5 S 24 5.16 5 C 8747 2.51 5 N 2825 2.21 5 O 3434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 5.020 Check model and map are aligned: 0.240 Process input model: 47.860 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 0.078 16208 Z= 0.404 Angle : 0.873 8.533 23159 Z= 0.504 Chirality : 0.050 0.317 2622 Planarity : 0.007 0.075 1924 Dihedral : 25.437 169.552 6543 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.19), residues: 1126 helix: -2.61 (0.15), residues: 599 sheet: -2.24 (0.55), residues: 70 loop : -2.66 (0.25), residues: 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 1.449 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 324 average time/residue: 0.4332 time to fit residues: 180.7353 Evaluate side-chains 188 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1300 time to fit residues: 1.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN G 112 GLN K 181 HIS A 68 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN C 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16208 Z= 0.191 Angle : 0.566 5.767 23159 Z= 0.328 Chirality : 0.035 0.138 2622 Planarity : 0.005 0.048 1924 Dihedral : 28.416 167.318 4235 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.22 (0.23), residues: 1126 helix: -0.89 (0.19), residues: 629 sheet: -1.42 (0.57), residues: 63 loop : -2.24 (0.27), residues: 434 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.345 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 237 average time/residue: 0.3721 time to fit residues: 122.1621 Evaluate side-chains 204 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1493 time to fit residues: 8.1091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS E 93 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 16208 Z= 0.272 Angle : 0.593 5.745 23159 Z= 0.339 Chirality : 0.037 0.150 2622 Planarity : 0.005 0.037 1924 Dihedral : 28.840 167.429 4235 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.24), residues: 1126 helix: -0.45 (0.20), residues: 640 sheet: -0.74 (0.65), residues: 63 loop : -1.83 (0.29), residues: 423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 205 average time/residue: 0.3554 time to fit residues: 99.8681 Evaluate side-chains 181 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1347 time to fit residues: 6.5436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 30 HIS L 62 GLN L 68 HIS ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 16208 Z= 0.198 Angle : 0.534 5.501 23159 Z= 0.310 Chirality : 0.035 0.137 2622 Planarity : 0.004 0.035 1924 Dihedral : 28.711 165.495 4235 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.25), residues: 1126 helix: 0.09 (0.21), residues: 637 sheet: -0.51 (0.66), residues: 63 loop : -1.51 (0.30), residues: 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 180 average time/residue: 0.3460 time to fit residues: 86.3391 Evaluate side-chains 167 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1926 time to fit residues: 4.0531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN L 68 HIS ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN B 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 16208 Z= 0.271 Angle : 0.574 6.347 23159 Z= 0.329 Chirality : 0.037 0.143 2622 Planarity : 0.004 0.036 1924 Dihedral : 28.910 165.860 4235 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.25), residues: 1126 helix: 0.14 (0.21), residues: 638 sheet: -0.56 (0.67), residues: 63 loop : -1.30 (0.31), residues: 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.422 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 186 average time/residue: 0.3583 time to fit residues: 92.7755 Evaluate side-chains 173 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1386 time to fit residues: 3.9647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 78 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.161 Angle : 0.515 5.447 23159 Z= 0.301 Chirality : 0.034 0.138 2622 Planarity : 0.004 0.039 1924 Dihedral : 28.672 163.260 4235 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.26), residues: 1126 helix: 0.53 (0.21), residues: 641 sheet: -0.37 (0.67), residues: 64 loop : -1.11 (0.31), residues: 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 1.309 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 179 average time/residue: 0.3665 time to fit residues: 89.6888 Evaluate side-chains 168 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1336 time to fit residues: 2.4000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 181 HIS ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.176 Angle : 0.524 9.941 23159 Z= 0.304 Chirality : 0.034 0.138 2622 Planarity : 0.004 0.038 1924 Dihedral : 28.705 162.831 4235 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.26), residues: 1126 helix: 0.65 (0.22), residues: 634 sheet: -0.20 (0.69), residues: 64 loop : -0.97 (0.31), residues: 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 1.338 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 172 average time/residue: 0.3451 time to fit residues: 82.5567 Evaluate side-chains 163 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1367 time to fit residues: 2.6341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 85 optimal weight: 0.2980 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 105 optimal weight: 0.1980 chunk 121 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN D 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.148 Angle : 0.513 10.775 23159 Z= 0.297 Chirality : 0.033 0.134 2622 Planarity : 0.004 0.041 1924 Dihedral : 28.532 160.828 4235 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.26), residues: 1126 helix: 0.91 (0.22), residues: 632 sheet: -0.15 (0.69), residues: 63 loop : -0.82 (0.31), residues: 431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 1.317 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 184 average time/residue: 0.3328 time to fit residues: 85.8026 Evaluate side-chains 166 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1659 time to fit residues: 1.8008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.162 Angle : 0.514 7.835 23159 Z= 0.298 Chirality : 0.033 0.134 2622 Planarity : 0.004 0.040 1924 Dihedral : 28.595 161.019 4235 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.26), residues: 1126 helix: 0.98 (0.22), residues: 634 sheet: -0.01 (0.68), residues: 64 loop : -0.71 (0.32), residues: 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.303 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 167 average time/residue: 0.3454 time to fit residues: 80.0108 Evaluate side-chains 161 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1590 time to fit residues: 2.2900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 138 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 16208 Z= 0.388 Angle : 0.643 10.231 23159 Z= 0.361 Chirality : 0.040 0.153 2622 Planarity : 0.005 0.035 1924 Dihedral : 29.239 164.916 4235 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.26), residues: 1126 helix: 0.41 (0.21), residues: 639 sheet: -0.23 (0.69), residues: 64 loop : -0.93 (0.31), residues: 423 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.391 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.3631 time to fit residues: 79.5871 Evaluate side-chains 157 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1472 time to fit residues: 2.7360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.151169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106193 restraints weight = 21904.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106674 restraints weight = 19261.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106821 restraints weight = 17143.892| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16208 Z= 0.184 Angle : 0.540 10.729 23159 Z= 0.313 Chirality : 0.034 0.139 2622 Planarity : 0.004 0.038 1924 Dihedral : 28.861 163.005 4235 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.26), residues: 1126 helix: 0.73 (0.22), residues: 637 sheet: -0.21 (0.70), residues: 64 loop : -0.81 (0.31), residues: 425 =============================================================================== Job complete usr+sys time: 2619.20 seconds wall clock time: 48 minutes 10.75 seconds (2890.75 seconds total)