Starting phenix.real_space_refine on Sat Mar 16 11:30:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn8_40616/03_2024/8sn8_40616.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn8_40616/03_2024/8sn8_40616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn8_40616/03_2024/8sn8_40616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn8_40616/03_2024/8sn8_40616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn8_40616/03_2024/8sn8_40616.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn8_40616/03_2024/8sn8_40616.pdb" } resolution = 3.7 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8269 2.51 5 N 2713 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14600 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 34.250 72.890 43.549 1.00 74.78 S ATOM 12446 SG CYS K 51 31.943 69.964 43.371 1.00 65.34 S ATOM 12470 SG CYS K 54 34.443 70.787 40.404 1.00 80.92 S ATOM 12187 SG CYS K 16 21.836 69.400 49.197 1.00 88.95 S ATOM 12205 SG CYS K 19 19.480 67.747 51.492 1.00 90.04 S ATOM 12335 SG CYS K 36 22.401 69.913 52.882 1.00 73.23 S ATOM 12357 SG CYS K 39 23.142 66.555 51.678 1.00 76.19 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 8.47, per 1000 atoms: 0.58 Number of scatterers: 14600 At special positions: 0 Unit cell: (110.224, 132.8, 127.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3289 8.00 N 2713 7.00 C 8269 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: 6.80 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " Number of angles added : 9 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 62.6% alpha, 5.3% beta 135 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 5.90 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.546A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.556A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) 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 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.912A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.848A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.710A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.693A 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 removed outlier: 3.542A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.578A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.545A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.685A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.796A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.960A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.598A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.805A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.729A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 removed outlier: 3.667A pdb=" N SER K 42 " --> pdb=" O PRO K 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL K 44 " --> pdb=" O PHE K 40 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS K 46 " --> pdb=" O SER K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.800A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 4.054A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.586A pdb=" N ASP L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.267A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 86 through 91' Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.642A pdb=" N ASP L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.530A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 147 removed outlier: 3.550A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET L 147 " --> pdb=" O GLN L 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.862A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.878A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 101 through 102 removed outlier: 6.789A 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: 7.187A 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: 7.737A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16 492 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3565 1.34 - 1.46: 4321 1.46 - 1.58: 6951 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" CB ARG K 55 " pdb=" CG ARG K 55 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CB ASP E 81 " pdb=" CG ASP E 81 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CA ASP E 81 " pdb=" CB ASP E 81 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.68e-01 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.90e-01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.65: 1549 105.65 - 112.76: 8614 112.76 - 119.87: 5333 119.87 - 126.98: 5913 126.98 - 134.09: 762 Bond angle restraints: 22171 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 120.97 -8.27 3.00e+00 1.11e-01 7.60e+00 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 121.54 126.55 -5.01 1.91e+00 2.74e-01 6.88e+00 angle pdb=" CB MET D 59 " pdb=" CG MET D 59 " pdb=" SD MET D 59 " ideal model delta sigma weight residual 112.70 105.03 7.67 3.00e+00 1.11e-01 6.53e+00 angle pdb=" C ALA L 14 " pdb=" N ARG L 15 " pdb=" CA ARG L 15 " ideal model delta sigma weight residual 121.58 117.14 4.44 1.95e+00 2.63e-01 5.19e+00 angle pdb=" N ASP E 81 " pdb=" CA ASP E 81 " pdb=" C ASP E 81 " ideal model delta sigma weight residual 110.80 115.63 -4.83 2.13e+00 2.20e-01 5.13e+00 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 7273 35.54 - 71.07: 1314 71.07 - 106.61: 16 106.61 - 142.14: 0 142.14 - 177.68: 2 Dihedral angle restraints: 8605 sinusoidal: 5467 harmonic: 3138 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 37.68 -177.68 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 74.80 145.20 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA PHE K 53 " pdb=" C PHE K 53 " pdb=" N CYS K 54 " pdb=" CA CYS K 54 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1919 0.035 - 0.069: 450 0.069 - 0.104: 110 0.104 - 0.138: 35 0.138 - 0.173: 2 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CB ILE D 94 " pdb=" CA ILE D 94 " pdb=" CG1 ILE D 94 " pdb=" CG2 ILE D 94 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA GLU K 25 " pdb=" N GLU K 25 " pdb=" C GLU K 25 " pdb=" CB GLU K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2513 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 55 " 0.146 9.50e-02 1.11e+02 6.56e-02 2.79e+00 pdb=" NE ARG K 55 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG K 55 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG K 55 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG K 55 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO D 103 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO K 38 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.022 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1954 2.76 - 3.47: 19627 3.47 - 4.19: 38241 4.19 - 4.90: 59638 Nonbonded interactions: 119462 Sorted by model distance: nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.331 3.350 nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.332 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.185 2.496 nonbonded pdb=" N SER C 11 " pdb=" O SER D 123 " model vdw 2.246 2.520 nonbonded pdb=" N SER G 11 " pdb=" O SER H 123 " model vdw 2.255 2.520 ... (remaining 119457 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' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.17 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: 1.040 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: 4.210 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 46.510 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.003 0.034 15472 Z= 0.179 Angle : 0.545 8.271 22171 Z= 0.318 Chirality : 0.034 0.173 2516 Planarity : 0.004 0.066 1794 Dihedral : 25.620 177.679 6577 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.26), residues: 1057 helix: 2.45 (0.21), residues: 629 sheet: 1.04 (0.72), residues: 50 loop : -0.47 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS B 75 PHE 0.014 0.001 PHE M 4 TYR 0.018 0.001 TYR H 40 ARG 0.007 0.000 ARG K 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8553 (ttmm) REVERT: G 23 LEU cc_start: 0.9114 (mt) cc_final: 0.8768 (mt) REVERT: G 76 THR cc_start: 0.9088 (p) cc_final: 0.8823 (t) REVERT: G 78 ILE cc_start: 0.9207 (mm) cc_final: 0.8968 (mm) REVERT: H 120 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8872 (tttp) REVERT: L 3 LEU cc_start: 0.8855 (mm) cc_final: 0.8636 (mm) REVERT: L 55 HIS cc_start: 0.7037 (m-70) cc_final: 0.6747 (m-70) REVERT: M 1 MET cc_start: 0.3502 (ttt) cc_final: 0.1500 (tpt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3498 time to fit residues: 107.8050 Evaluate side-chains 188 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 0.0770 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS L 32 HIS ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15472 Z= 0.208 Angle : 0.563 11.880 22171 Z= 0.323 Chirality : 0.035 0.184 2516 Planarity : 0.004 0.039 1794 Dihedral : 28.738 177.545 4413 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.84 % Allowed : 10.17 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.97 (0.26), residues: 1057 helix: 2.32 (0.20), residues: 647 sheet: 0.99 (0.71), residues: 50 loop : -0.56 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 33 HIS 0.002 0.001 HIS B 75 PHE 0.011 0.001 PHE L 69 TYR 0.020 0.002 TYR K 84 ARG 0.006 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8613 (ttmm) REVERT: G 23 LEU cc_start: 0.9156 (mt) cc_final: 0.8806 (mt) REVERT: G 76 THR cc_start: 0.9151 (p) cc_final: 0.8829 (t) REVERT: G 78 ILE cc_start: 0.9359 (mm) cc_final: 0.9127 (mm) REVERT: H 85 LYS cc_start: 0.8882 (mttp) cc_final: 0.8598 (mtmm) REVERT: H 120 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8984 (tttp) REVERT: L 8 LYS cc_start: 0.8978 (tptm) cc_final: 0.8647 (tptp) outliers start: 17 outliers final: 13 residues processed: 210 average time/residue: 0.3278 time to fit residues: 93.5725 Evaluate side-chains 201 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15472 Z= 0.345 Angle : 0.610 11.492 22171 Z= 0.347 Chirality : 0.037 0.173 2516 Planarity : 0.005 0.043 1794 Dihedral : 29.061 176.978 4413 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.25 % Allowed : 12.23 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.67 (0.26), residues: 1057 helix: 2.11 (0.20), residues: 645 sheet: 0.85 (0.71), residues: 50 loop : -0.73 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP L 33 HIS 0.004 0.001 HIS E 113 PHE 0.017 0.002 PHE H 70 TYR 0.029 0.002 TYR D 83 ARG 0.005 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.8877 (tpt) cc_final: 0.8578 (tpp) REVERT: D 116 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8577 (ttmm) REVERT: G 23 LEU cc_start: 0.9200 (mt) cc_final: 0.8882 (mt) REVERT: G 78 ILE cc_start: 0.9468 (mm) cc_final: 0.9235 (mm) REVERT: L 8 LYS cc_start: 0.8901 (tptm) cc_final: 0.8586 (tptm) outliers start: 30 outliers final: 25 residues processed: 205 average time/residue: 0.3295 time to fit residues: 92.1110 Evaluate side-chains 209 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15472 Z= 0.206 Angle : 0.560 11.439 22171 Z= 0.321 Chirality : 0.035 0.166 2516 Planarity : 0.004 0.042 1794 Dihedral : 28.990 177.785 4413 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.25 % Allowed : 13.42 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.86 (0.26), residues: 1057 helix: 2.28 (0.20), residues: 648 sheet: 0.80 (0.69), residues: 50 loop : -0.70 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP L 33 HIS 0.003 0.001 HIS L 55 PHE 0.008 0.001 PHE E 104 TYR 0.027 0.002 TYR D 83 ARG 0.005 0.000 ARG K 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8754 (m-10) cc_final: 0.8051 (m-10) REVERT: D 59 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8415 (tpp) REVERT: D 83 TYR cc_start: 0.7570 (m-80) cc_final: 0.6650 (m-80) REVERT: D 116 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8568 (ttmm) REVERT: G 23 LEU cc_start: 0.9193 (mt) cc_final: 0.8851 (mt) REVERT: G 78 ILE cc_start: 0.9424 (mm) cc_final: 0.9152 (mm) REVERT: G 95 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8723 (tttt) REVERT: L 8 LYS cc_start: 0.8904 (tptm) cc_final: 0.8568 (tptm) outliers start: 30 outliers final: 24 residues processed: 203 average time/residue: 0.3253 time to fit residues: 89.9280 Evaluate side-chains 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15472 Z= 0.230 Angle : 0.559 10.899 22171 Z= 0.322 Chirality : 0.035 0.160 2516 Planarity : 0.004 0.042 1794 Dihedral : 29.054 177.564 4413 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.68 % Allowed : 13.31 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.84 (0.26), residues: 1057 helix: 2.29 (0.20), residues: 647 sheet: 0.74 (0.69), residues: 50 loop : -0.74 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP L 33 HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE H 70 TYR 0.028 0.002 TYR D 83 ARG 0.007 0.000 ARG L 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8348 (tpp) REVERT: D 116 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8600 (ttmm) REVERT: F 84 MET cc_start: 0.8600 (mmm) cc_final: 0.8380 (mmm) REVERT: G 23 LEU cc_start: 0.9180 (mt) cc_final: 0.8842 (mt) REVERT: G 78 ILE cc_start: 0.9435 (mm) cc_final: 0.9152 (mm) REVERT: G 95 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8726 (tttt) REVERT: L 8 LYS cc_start: 0.8887 (tptm) cc_final: 0.8542 (tptm) outliers start: 34 outliers final: 28 residues processed: 206 average time/residue: 0.3143 time to fit residues: 88.6917 Evaluate side-chains 214 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 0.0670 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN L 20 GLN L 32 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15472 Z= 0.178 Angle : 0.543 10.987 22171 Z= 0.313 Chirality : 0.034 0.173 2516 Planarity : 0.004 0.052 1794 Dihedral : 29.004 177.807 4413 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.46 % Allowed : 14.18 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.96 (0.26), residues: 1057 helix: 2.40 (0.20), residues: 646 sheet: 0.77 (0.69), residues: 50 loop : -0.70 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 33 HIS 0.002 0.001 HIS A 39 PHE 0.011 0.001 PHE K 53 TYR 0.016 0.001 TYR H 121 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8303 (tpp) REVERT: D 116 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8594 (ttmm) REVERT: G 23 LEU cc_start: 0.9171 (mt) cc_final: 0.8834 (mt) REVERT: G 76 THR cc_start: 0.9160 (p) cc_final: 0.8779 (t) REVERT: G 78 ILE cc_start: 0.9393 (mm) cc_final: 0.9090 (mm) REVERT: G 95 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8709 (tttt) REVERT: L 8 LYS cc_start: 0.8830 (tptm) cc_final: 0.8491 (tptm) outliers start: 32 outliers final: 25 residues processed: 206 average time/residue: 0.3118 time to fit residues: 88.1170 Evaluate side-chains 212 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN L 32 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15472 Z= 0.207 Angle : 0.561 10.890 22171 Z= 0.320 Chirality : 0.034 0.163 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.041 177.516 4413 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.46 % Allowed : 15.37 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.96 (0.26), residues: 1057 helix: 2.38 (0.20), residues: 648 sheet: 0.84 (0.70), residues: 50 loop : -0.70 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 33 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE K 53 TYR 0.024 0.001 TYR D 83 ARG 0.011 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8291 (tpp) REVERT: D 116 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8603 (ttmm) REVERT: F 84 MET cc_start: 0.8638 (mmm) cc_final: 0.8422 (mmm) REVERT: G 23 LEU cc_start: 0.9172 (mt) cc_final: 0.8825 (mt) REVERT: G 78 ILE cc_start: 0.9411 (mm) cc_final: 0.9111 (mm) REVERT: G 95 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8711 (tttt) REVERT: L 8 LYS cc_start: 0.8879 (tptm) cc_final: 0.8551 (tptm) outliers start: 32 outliers final: 27 residues processed: 205 average time/residue: 0.3325 time to fit residues: 93.8310 Evaluate side-chains 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15472 Z= 0.203 Angle : 0.562 10.919 22171 Z= 0.320 Chirality : 0.034 0.171 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.031 177.611 4413 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.57 % Allowed : 15.48 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.96 (0.26), residues: 1057 helix: 2.38 (0.20), residues: 650 sheet: 0.78 (0.69), residues: 50 loop : -0.71 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 33 HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE H 70 TYR 0.026 0.002 TYR D 83 ARG 0.006 0.000 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8501 (m-10) cc_final: 0.7704 (m-10) REVERT: D 59 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8278 (tpp) REVERT: D 116 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8602 (ttmm) REVERT: G 23 LEU cc_start: 0.9165 (mt) cc_final: 0.8820 (mt) REVERT: G 78 ILE cc_start: 0.9404 (mm) cc_final: 0.9100 (mm) REVERT: G 95 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8712 (tttt) REVERT: K 56 ARG cc_start: 0.8575 (tpp80) cc_final: 0.8282 (tpp80) outliers start: 33 outliers final: 28 residues processed: 202 average time/residue: 0.3047 time to fit residues: 85.2371 Evaluate side-chains 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15472 Z= 0.221 Angle : 0.575 10.936 22171 Z= 0.324 Chirality : 0.035 0.172 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.059 177.532 4413 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.46 % Allowed : 15.91 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.92 (0.26), residues: 1057 helix: 2.37 (0.20), residues: 649 sheet: 0.57 (0.68), residues: 50 loop : -0.74 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 33 HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE H 70 TYR 0.029 0.002 TYR D 83 ARG 0.010 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8331 (tpp) REVERT: D 116 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8608 (ttmm) REVERT: G 23 LEU cc_start: 0.9169 (mt) cc_final: 0.8821 (mt) REVERT: G 78 ILE cc_start: 0.9418 (mm) cc_final: 0.9121 (mm) REVERT: G 95 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8722 (tttt) REVERT: L 78 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8461 (tp) outliers start: 32 outliers final: 27 residues processed: 207 average time/residue: 0.3142 time to fit residues: 89.0828 Evaluate side-chains 214 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.0020 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15472 Z= 0.194 Angle : 0.567 10.874 22171 Z= 0.320 Chirality : 0.034 0.168 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.018 177.641 4413 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.46 % Allowed : 15.91 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.95 (0.26), residues: 1057 helix: 2.38 (0.20), residues: 651 sheet: 0.49 (0.68), residues: 50 loop : -0.70 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 33 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE H 70 TYR 0.027 0.001 TYR D 83 ARG 0.010 0.000 ARG L 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8521 (m-10) cc_final: 0.7745 (m-10) REVERT: D 116 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8603 (ttmm) REVERT: G 23 LEU cc_start: 0.9156 (mt) cc_final: 0.8810 (mt) REVERT: G 78 ILE cc_start: 0.9400 (mm) cc_final: 0.9101 (mm) REVERT: G 95 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8713 (tttt) REVERT: L 78 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8471 (tp) REVERT: L 145 TYR cc_start: 0.5333 (OUTLIER) cc_final: 0.5045 (m-10) outliers start: 32 outliers final: 27 residues processed: 204 average time/residue: 0.3007 time to fit residues: 84.7609 Evaluate side-chains 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098481 restraints weight = 37894.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.101998 restraints weight = 67652.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102520 restraints weight = 25083.229| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15472 Z= 0.197 Angle : 0.579 10.895 22171 Z= 0.325 Chirality : 0.034 0.164 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.011 177.616 4413 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.35 % Allowed : 16.67 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.96 (0.26), residues: 1057 helix: 2.41 (0.21), residues: 651 sheet: 0.43 (0.68), residues: 50 loop : -0.71 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 33 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE H 70 TYR 0.029 0.002 TYR D 83 ARG 0.010 0.000 ARG L 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2571.65 seconds wall clock time: 47 minutes 1.77 seconds (2821.77 seconds total)