Starting phenix.real_space_refine on Tue Apr 9 12:31:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux1_42685/04_2024/8ux1_42685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux1_42685/04_2024/8ux1_42685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux1_42685/04_2024/8ux1_42685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux1_42685/04_2024/8ux1_42685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux1_42685/04_2024/8ux1_42685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux1_42685/04_2024/8ux1_42685.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 sd= 0.209 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: 5 Type Number sf(0) Gaussians P 291 5.49 5 S 35 5.16 5 C 9407 2.51 5 N 3040 2.21 5 O 3622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "L ASP 136": "OD1" <-> "OD2" Residue "L ASP 182": "OD1" <-> "OD2" Residue "L ASP 244": "OD1" <-> "OD2" Residue "L TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 310": "OD1" <-> "OD2" Residue "L GLU 312": "OE1" <-> "OE2" Residue "L GLU 333": "OE1" <-> "OE2" Residue "L ASP 363": "OD1" <-> "OD2" Residue "L GLU 383": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16395 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 771 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 771 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2991 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2976 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1310 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain breaks: 2 Chain: "L" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2975 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 14, 'TRANS': 383} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LYS C 13 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 13 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 8.55, per 1000 atoms: 0.52 Number of scatterers: 16395 At special positions: 0 Unit cell: (144.2, 117.42, 115.36, 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 35 16.00 P 291 15.00 O 3622 8.00 N 3040 7.00 C 9407 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: 7.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 19 sheets defined 47.2% alpha, 14.1% beta 141 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.726A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.288A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.557A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.333A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 removed outlier: 3.570A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 28 Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 77 through 82 removed outlier: 4.521A pdb=" N GLN K 82 " --> pdb=" O GLY K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 99 Processing helix chain 'K' and resid 100 through 112 Processing helix chain 'K' and resid 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' Processing helix chain 'K' and resid 135 through 141 removed outlier: 3.601A pdb=" N HIS K 139 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG K 140 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS K 141 " --> pdb=" O VAL K 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 135 through 141' Processing helix chain 'K' and resid 158 through 170 Processing helix chain 'L' and resid 107 through 111 removed outlier: 3.792A pdb=" N VAL L 111 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 225 Processing helix chain 'L' and resid 321 through 325 removed outlier: 3.595A pdb=" N GLY L 324 " --> pdb=" O ALA L 321 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG L 325 " --> pdb=" O GLU L 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 321 through 325' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.775A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.655A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.324A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.467A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.826A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.347A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 48 through 49 removed outlier: 7.484A pdb=" N VAL K 9 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASN K 62 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE K 11 " --> pdb=" O ASN K 62 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TRP K 64 " --> pdb=" O PHE K 11 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU K 13 " --> pdb=" O TRP K 64 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN K 145 " --> pdb=" O ILE K 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 56 through 63 removed outlier: 6.073A pdb=" N LYS L 59 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR L 39 " --> pdb=" O LYS L 59 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA L 61 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL L 37 " --> pdb=" O ALA L 61 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS L 410 " --> pdb=" O SER L 406 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER L 406 " --> pdb=" O HIS L 410 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL L 412 " --> pdb=" O VAL L 404 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL L 404 " --> pdb=" O VAL L 412 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU L 414 " --> pdb=" O LEU L 402 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 69 through 74 Processing sheet with id=AB5, first strand: chain 'L' and resid 121 through 126 Processing sheet with id=AB6, first strand: chain 'L' and resid 146 through 148 removed outlier: 6.141A pdb=" N PHE L 146 " --> pdb=" O ILE L 153 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY L 151 " --> pdb=" O ASP L 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 174 through 179 removed outlier: 3.778A pdb=" N LYS L 227 " --> pdb=" O THR L 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 242 through 247 removed outlier: 6.771A pdb=" N VAL L 261 " --> pdb=" O GLN L 284 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN L 284 " --> pdb=" O VAL L 261 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY L 263 " --> pdb=" O ILE L 282 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE L 282 " --> pdb=" O GLY L 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 296 through 301 removed outlier: 3.537A pdb=" N GLY L 298 " --> pdb=" O MET L 309 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLY L 319 " --> pdb=" O ILE L 337 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE L 337 " --> pdb=" O GLY L 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 347 through 352 removed outlier: 6.657A pdb=" N VAL L 360 " --> pdb=" O SER L 348 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL L 350 " --> pdb=" O TYR L 358 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR L 358 " --> pdb=" O VAL L 350 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS L 352 " --> pdb=" O VAL L 356 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL L 356 " --> pdb=" O CYS L 352 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY L 370 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER L 387 " --> pdb=" O GLY L 370 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 718 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 7.12 Time building geometry restraints manager: 7.70 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: 3283 1.33 - 1.45: 5045 1.45 - 1.57: 8326 1.57 - 1.69: 575 1.69 - 1.81: 59 Bond restraints: 17288 Sorted by residual: bond pdb=" CA SER L 288 " pdb=" CB SER L 288 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.56e-02 4.11e+03 9.78e+00 bond pdb=" O3' DG J 9 " pdb=" P DC J 10 " ideal model delta sigma weight residual 1.607 1.563 0.044 1.50e-02 4.44e+03 8.70e+00 bond pdb=" O3' DC J -4 " pdb=" P DG J -3 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.50e-02 4.44e+03 7.32e+00 bond pdb=" O3' DC J 8 " pdb=" P DG J 9 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.85e+00 bond pdb=" O3' DG I 8 " pdb=" P DT I 9 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.50e-02 4.44e+03 6.54e+00 ... (remaining 17283 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.83: 1663 105.83 - 112.87: 9387 112.87 - 119.91: 5902 119.91 - 126.95: 6843 126.95 - 133.99: 782 Bond angle restraints: 24577 Sorted by residual: angle pdb=" C2' DC J -10 " pdb=" C1' DC J -10 " pdb=" N1 DC J -10 " ideal model delta sigma weight residual 113.50 122.25 -8.75 1.50e+00 4.44e-01 3.41e+01 angle pdb=" C ALA K 151 " pdb=" N LYS K 152 " pdb=" CA LYS K 152 " ideal model delta sigma weight residual 122.46 116.51 5.95 1.41e+00 5.03e-01 1.78e+01 angle pdb=" N LYS K 152 " pdb=" CA LYS K 152 " pdb=" C LYS K 152 " ideal model delta sigma weight residual 111.30 106.20 5.10 1.36e+00 5.41e-01 1.40e+01 angle pdb=" CA GLN K 10 " pdb=" C GLN K 10 " pdb=" O GLN K 10 " ideal model delta sigma weight residual 121.11 117.30 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" CA LYS K 152 " pdb=" C LYS K 152 " pdb=" O LYS K 152 " ideal model delta sigma weight residual 122.03 118.28 3.75 1.17e+00 7.31e-01 1.03e+01 ... (remaining 24572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.01: 6989 20.01 - 40.02: 1475 40.02 - 60.03: 1083 60.03 - 80.04: 65 80.04 - 100.05: 7 Dihedral angle restraints: 9619 sinusoidal: 5823 harmonic: 3796 Sorted by residual: dihedral pdb=" CA CYS L 247 " pdb=" C CYS L 247 " pdb=" N GLY L 248 " pdb=" CA GLY L 248 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR K 80 " pdb=" C TYR K 80 " pdb=" N ILE K 81 " pdb=" CA ILE K 81 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA SER L 179 " pdb=" C SER L 179 " pdb=" N GLY L 180 " pdb=" CA GLY L 180 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 9616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2670 0.098 - 0.195: 94 0.195 - 0.293: 0 0.293 - 0.390: 0 0.390 - 0.488: 1 Chirality restraints: 2765 Sorted by residual: chirality pdb=" C1' DC J -10 " pdb=" O4' DC J -10 " pdb=" C2' DC J -10 " pdb=" N1 DC J -10 " both_signs ideal model delta sigma weight residual False 2.47 1.98 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA HIS K 139 " pdb=" N HIS K 139 " pdb=" C HIS K 139 " pdb=" CB HIS K 139 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 2762 not shown) Planarity restraints: 2119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.025 2.00e-02 2.50e+03 1.07e-02 3.45e+00 pdb=" N9 DG I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 14 " 0.023 2.00e-02 2.50e+03 1.15e-02 3.29e+00 pdb=" N1 DT I 14 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT I 14 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 14 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DT I 14 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 14 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT I 14 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 14 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 14 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 14 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -4 " 0.023 2.00e-02 2.50e+03 9.81e-03 2.89e+00 pdb=" N9 DG I -4 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -4 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I -4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I -4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -4 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG I -4 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I -4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -4 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -4 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -4 " -0.000 2.00e-02 2.50e+03 ... (remaining 2116 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 471 2.69 - 3.24: 14697 3.24 - 3.79: 30016 3.79 - 4.35: 40374 4.35 - 4.90: 58581 Nonbonded interactions: 144139 Sorted by model distance: nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.132 2.520 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.206 3.040 nonbonded pdb=" N GLU L 330 " pdb=" OE1 GLU L 330 " model vdw 2.213 2.520 nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.220 2.520 nonbonded pdb=" O ASP B 24 " pdb=" OD1 ASP B 24 " model vdw 2.222 3.040 ... (remaining 144134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = (chain 'G' and resid 13 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.070 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: 4.290 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 49.380 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:22.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.006 0.049 17288 Z= 0.346 Angle : 0.638 8.754 24577 Z= 0.388 Chirality : 0.044 0.488 2765 Planarity : 0.004 0.038 2119 Dihedral : 25.883 100.045 7189 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.22 % Favored : 97.55 % Rotamer: Outliers : 1.27 % Allowed : 14.83 % Favored : 83.91 % 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: 1.25 (0.24), residues: 1308 helix: 1.92 (0.22), residues: 595 sheet: 0.01 (0.42), residues: 166 loop : -0.05 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 163 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.002 PHE L 264 TYR 0.010 0.001 TYR E 54 ARG 0.003 0.000 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 1.394 Fit side-chains REVERT: C 92 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8052 (mt-10) REVERT: D 73 GLU cc_start: 0.8520 (tp30) cc_final: 0.8283 (tp30) REVERT: K 38 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6595 (mmtp) REVERT: K 110 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8117 (ttp-170) REVERT: K 152 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6930 (mppt) REVERT: L 394 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8017 (mmmt) outliers start: 14 outliers final: 5 residues processed: 201 average time/residue: 1.7780 time to fit residues: 387.9121 Evaluate side-chains 190 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 349 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.8980 chunk 117 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 106 HIS F 75 HIS ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17288 Z= 0.260 Angle : 0.563 5.595 24577 Z= 0.330 Chirality : 0.037 0.145 2765 Planarity : 0.004 0.036 2119 Dihedral : 28.748 118.492 4650 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 2.44 % Allowed : 14.20 % Favored : 83.36 % 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: 1.57 (0.23), residues: 1308 helix: 2.20 (0.21), residues: 601 sheet: 0.02 (0.40), residues: 161 loop : 0.13 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.004 0.001 HIS D 46 PHE 0.017 0.002 PHE A 67 TYR 0.015 0.001 TYR K 80 ARG 0.002 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.470 Fit side-chains REVERT: C 92 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: D 73 GLU cc_start: 0.8516 (tp30) cc_final: 0.8282 (tp30) REVERT: D 90 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: G 73 ASN cc_start: 0.8262 (t0) cc_final: 0.8033 (t160) REVERT: K 110 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8130 (ttp-170) REVERT: L 109 GLU cc_start: 0.7180 (pt0) cc_final: 0.6977 (pt0) REVERT: L 239 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7363 (p-80) outliers start: 27 outliers final: 5 residues processed: 199 average time/residue: 1.6744 time to fit residues: 363.0897 Evaluate side-chains 192 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN E 39 HIS E 113 HIS K 105 HIS L 42 GLN L 260 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17288 Z= 0.446 Angle : 0.611 5.442 24577 Z= 0.353 Chirality : 0.042 0.165 2765 Planarity : 0.005 0.071 2119 Dihedral : 28.883 125.169 4638 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 2.71 % Allowed : 16.73 % Favored : 80.56 % 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: 1.29 (0.23), residues: 1308 helix: 1.91 (0.21), residues: 605 sheet: 0.05 (0.40), residues: 166 loop : -0.03 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 163 HIS 0.006 0.002 HIS L 410 PHE 0.020 0.002 PHE K 26 TYR 0.014 0.002 TYR K 80 ARG 0.005 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 3.960 Fit side-chains REVERT: C 91 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: C 92 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: D 73 GLU cc_start: 0.8539 (tp30) cc_final: 0.8287 (tp30) REVERT: D 90 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: G 73 ASN cc_start: 0.8340 (t0) cc_final: 0.7992 (t160) REVERT: K 21 THR cc_start: 0.8530 (p) cc_final: 0.8320 (m) REVERT: K 136 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8249 (mp) REVERT: L 239 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7409 (p90) REVERT: L 322 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7568 (mp0) outliers start: 30 outliers final: 11 residues processed: 203 average time/residue: 1.7311 time to fit residues: 384.4019 Evaluate side-chains 199 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 81 ASN F 27 GLN G 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17288 Z= 0.225 Angle : 0.544 5.291 24577 Z= 0.321 Chirality : 0.037 0.137 2765 Planarity : 0.004 0.067 2119 Dihedral : 28.815 128.510 4638 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.99 % Favored : 97.94 % Rotamer: Outliers : 1.54 % Allowed : 18.26 % Favored : 80.20 % 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: 1.56 (0.23), residues: 1308 helix: 2.22 (0.21), residues: 599 sheet: 0.11 (0.40), residues: 161 loop : 0.06 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.010 0.001 HIS K 30 PHE 0.020 0.002 PHE K 26 TYR 0.014 0.001 TYR G 57 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.275 Fit side-chains REVERT: C 92 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: D 73 GLU cc_start: 0.8511 (tp30) cc_final: 0.8242 (tp30) REVERT: D 90 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: G 73 ASN cc_start: 0.8327 (t0) cc_final: 0.7931 (t160) REVERT: H 83 ARG cc_start: 0.8529 (mmt90) cc_final: 0.8276 (mmt90) REVERT: K 136 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8238 (mp) REVERT: L 381 GLN cc_start: 0.8478 (mm110) cc_final: 0.8221 (mm110) outliers start: 17 outliers final: 7 residues processed: 197 average time/residue: 1.6701 time to fit residues: 359.0619 Evaluate side-chains 193 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 0.0670 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 76 GLN C 104 GLN D 81 ASN F 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17288 Z= 0.245 Angle : 0.532 6.630 24577 Z= 0.315 Chirality : 0.036 0.149 2765 Planarity : 0.004 0.068 2119 Dihedral : 28.604 133.204 4638 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 2.35 % Allowed : 18.54 % Favored : 79.11 % 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: 1.66 (0.23), residues: 1308 helix: 2.34 (0.21), residues: 599 sheet: 0.12 (0.40), residues: 161 loop : 0.07 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.004 0.001 HIS K 30 PHE 0.026 0.002 PHE L 91 TYR 0.012 0.001 TYR K 80 ARG 0.003 0.000 ARG L 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 1.386 Fit side-chains REVERT: C 92 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: D 73 GLU cc_start: 0.8526 (tp30) cc_final: 0.8301 (tp30) REVERT: D 90 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: G 73 ASN cc_start: 0.8357 (t0) cc_final: 0.7943 (t160) REVERT: K 136 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8252 (mp) REVERT: L 239 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7333 (p-80) REVERT: L 322 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7508 (mp0) outliers start: 26 outliers final: 10 residues processed: 200 average time/residue: 1.6375 time to fit residues: 356.9426 Evaluate side-chains 199 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 78 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 81 ASN F 27 GLN ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17288 Z= 0.236 Angle : 0.529 7.763 24577 Z= 0.312 Chirality : 0.036 0.177 2765 Planarity : 0.004 0.071 2119 Dihedral : 28.545 134.071 4638 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.86 % Rotamer: Outliers : 1.81 % Allowed : 19.44 % Favored : 78.75 % 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: 1.70 (0.23), residues: 1308 helix: 2.38 (0.21), residues: 599 sheet: 0.10 (0.40), residues: 161 loop : 0.09 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS L 410 PHE 0.025 0.002 PHE L 91 TYR 0.012 0.001 TYR G 57 ARG 0.007 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.375 Fit side-chains REVERT: D 73 GLU cc_start: 0.8526 (tp30) cc_final: 0.8302 (tp30) REVERT: D 90 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: G 73 ASN cc_start: 0.8374 (t0) cc_final: 0.7967 (t160) REVERT: K 136 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8225 (mp) REVERT: L 175 VAL cc_start: 0.8545 (m) cc_final: 0.8298 (p) REVERT: L 239 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7345 (p-80) REVERT: L 322 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: L 381 GLN cc_start: 0.8503 (mm110) cc_final: 0.8198 (mm110) outliers start: 20 outliers final: 12 residues processed: 201 average time/residue: 1.5827 time to fit residues: 349.1813 Evaluate side-chains 203 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.1980 chunk 85 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 27 GLN G 19 ASN L 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17288 Z= 0.324 Angle : 0.560 8.085 24577 Z= 0.327 Chirality : 0.038 0.169 2765 Planarity : 0.004 0.074 2119 Dihedral : 28.691 134.062 4638 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 2.17 % Allowed : 19.44 % Favored : 78.39 % 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 (0.23), residues: 1308 helix: 2.23 (0.21), residues: 599 sheet: 0.09 (0.41), residues: 161 loop : 0.00 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 163 HIS 0.005 0.001 HIS L 410 PHE 0.030 0.002 PHE L 91 TYR 0.012 0.002 TYR K 80 ARG 0.007 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.315 Fit side-chains REVERT: D 73 GLU cc_start: 0.8535 (tp30) cc_final: 0.8267 (tp30) REVERT: D 90 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: G 73 ASN cc_start: 0.8381 (t0) cc_final: 0.7973 (t160) REVERT: K 168 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6210 (mt) REVERT: L 57 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6646 (mpt-90) REVERT: L 239 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7402 (p-80) REVERT: L 309 MET cc_start: 0.8352 (ttp) cc_final: 0.8030 (ttt) REVERT: L 322 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: L 381 GLN cc_start: 0.8500 (mm110) cc_final: 0.8176 (mm110) outliers start: 24 outliers final: 14 residues processed: 196 average time/residue: 1.6475 time to fit residues: 351.3782 Evaluate side-chains 205 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 135 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 81 ASN F 27 GLN G 19 ASN L 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17288 Z= 0.203 Angle : 0.549 10.633 24577 Z= 0.320 Chirality : 0.036 0.172 2765 Planarity : 0.004 0.076 2119 Dihedral : 28.699 134.315 4638 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 1.72 % Allowed : 20.34 % Favored : 77.94 % 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: 1.63 (0.23), residues: 1308 helix: 2.35 (0.21), residues: 599 sheet: 0.04 (0.41), residues: 161 loop : 0.03 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS F 75 PHE 0.029 0.002 PHE L 91 TYR 0.011 0.001 TYR K 80 ARG 0.007 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.446 Fit side-chains REVERT: D 73 GLU cc_start: 0.8523 (tp30) cc_final: 0.8265 (tp30) REVERT: G 73 ASN cc_start: 0.8383 (t0) cc_final: 0.7956 (t160) REVERT: K 148 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7144 (m-30) REVERT: K 168 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6128 (mt) REVERT: L 175 VAL cc_start: 0.8557 (m) cc_final: 0.8306 (p) REVERT: L 239 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7365 (p-80) REVERT: L 309 MET cc_start: 0.8342 (ttp) cc_final: 0.8018 (ttt) REVERT: L 322 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: L 381 GLN cc_start: 0.8501 (mm110) cc_final: 0.8172 (mm110) REVERT: L 394 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7990 (tptp) outliers start: 19 outliers final: 10 residues processed: 196 average time/residue: 1.6397 time to fit residues: 350.5015 Evaluate side-chains 198 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 148 ASP Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 125 optimal weight: 0.0040 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 27 GLN ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17288 Z= 0.195 Angle : 0.540 11.204 24577 Z= 0.317 Chirality : 0.036 0.137 2765 Planarity : 0.004 0.075 2119 Dihedral : 28.661 134.609 4638 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.36 % Allowed : 20.71 % Favored : 77.94 % 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: 1.66 (0.23), residues: 1308 helix: 2.40 (0.21), residues: 599 sheet: 0.05 (0.42), residues: 156 loop : 0.01 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 PHE 0.034 0.002 PHE L 91 TYR 0.016 0.001 TYR L 316 ARG 0.011 0.000 ARG L 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.354 Fit side-chains REVERT: D 73 GLU cc_start: 0.8522 (tp30) cc_final: 0.8284 (tp30) REVERT: G 73 ASN cc_start: 0.8383 (t0) cc_final: 0.7959 (t160) REVERT: K 168 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.6086 (mt) REVERT: L 175 VAL cc_start: 0.8550 (m) cc_final: 0.8300 (p) REVERT: L 239 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7354 (p-80) REVERT: L 309 MET cc_start: 0.8320 (ttp) cc_final: 0.7988 (ttt) REVERT: L 322 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: L 394 LYS cc_start: 0.8276 (mmmm) cc_final: 0.7983 (tptp) outliers start: 15 outliers final: 10 residues processed: 196 average time/residue: 1.6254 time to fit residues: 347.3487 Evaluate side-chains 199 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 142 optimal weight: 0.0470 chunk 122 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 27 GLN L 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17288 Z= 0.300 Angle : 0.556 11.019 24577 Z= 0.324 Chirality : 0.037 0.151 2765 Planarity : 0.004 0.079 2119 Dihedral : 28.659 135.388 4638 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.36 % Allowed : 20.80 % Favored : 77.85 % 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: 1.56 (0.23), residues: 1308 helix: 2.29 (0.21), residues: 599 sheet: 0.05 (0.41), residues: 161 loop : -0.02 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.004 0.001 HIS L 410 PHE 0.037 0.002 PHE L 91 TYR 0.015 0.001 TYR G 57 ARG 0.008 0.000 ARG H 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.488 Fit side-chains REVERT: D 73 GLU cc_start: 0.8537 (tp30) cc_final: 0.8275 (tp30) REVERT: G 73 ASN cc_start: 0.8394 (t0) cc_final: 0.7975 (t160) REVERT: L 128 ASP cc_start: 0.7796 (t0) cc_final: 0.7523 (t0) REVERT: L 239 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.7312 (p-80) REVERT: L 309 MET cc_start: 0.8308 (ttp) cc_final: 0.7978 (ttt) REVERT: L 322 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: L 394 LYS cc_start: 0.8293 (mmmm) cc_final: 0.8000 (tptp) outliers start: 15 outliers final: 10 residues processed: 198 average time/residue: 1.6377 time to fit residues: 354.2511 Evaluate side-chains 200 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.0270 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 27 GLN L 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089920 restraints weight = 24201.243| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.39 r_work: 0.3181 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.003 0.036 17288 Z= 0.177 Angle : 0.541 12.383 24577 Z= 0.317 Chirality : 0.035 0.137 2765 Planarity : 0.004 0.079 2119 Dihedral : 28.665 135.508 4636 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.45 % Allowed : 20.98 % Favored : 77.58 % 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: 1.65 (0.23), residues: 1308 helix: 2.43 (0.21), residues: 599 sheet: -0.17 (0.41), residues: 161 loop : 0.03 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS B 75 PHE 0.040 0.002 PHE L 91 TYR 0.012 0.001 TYR L 316 ARG 0.008 0.000 ARG L 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6068.01 seconds wall clock time: 109 minutes 27.82 seconds (6567.82 seconds total)