Starting phenix.real_space_refine on Sat Mar 16 11:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn6_40614/03_2024/8sn6_40614.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn6_40614/03_2024/8sn6_40614.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/8sn6_40614/03_2024/8sn6_40614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn6_40614/03_2024/8sn6_40614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn6_40614/03_2024/8sn6_40614.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn6_40614/03_2024/8sn6_40614.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 "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K GLU 25": "OE1" <-> "OE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 74": "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 32.578 74.262 46.883 1.00 88.39 S ATOM 12446 SG CYS K 51 31.271 71.186 45.070 1.00 91.68 S ATOM 12470 SG CYS K 54 32.612 74.141 43.059 1.00 96.59 S ATOM 12187 SG CYS K 16 22.251 68.673 52.194 1.00104.88 S ATOM 12205 SG CYS K 19 20.908 65.621 54.027 1.00100.49 S ATOM 12335 SG CYS K 36 23.441 67.769 55.828 1.00 94.61 S ATOM 12357 SG CYS K 39 24.460 65.513 53.151 1.00 91.60 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: 8.55, per 1000 atoms: 0.59 Number of scatterers: 14600 At special positions: 0 Unit cell: (110.224, 134.128, 126.16, 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: 7.40 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 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " 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: 46 helices and 13 sheets defined 62.9% alpha, 5.9% beta 135 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.587A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.560A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.873A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.846A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.504A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.564A 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 46 through 73 removed outlier: 3.672A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.539A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.824A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.600A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 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 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.029A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.529A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 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 90 through 97 removed outlier: 3.696A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.697A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.775A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 10 through 15 removed outlier: 3.806A pdb=" N CYS K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 15' Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.749A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.502A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE K 80 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN K 81 " --> pdb=" O TRP K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.859A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.686A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.926A pdb=" N VAL L 102 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU L 103 " --> pdb=" O ILE L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.921A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 3.918A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.612A 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: 6.768A 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: 8.117A 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: 6.996A 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: 7.254A 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: 7.813A 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 removed outlier: 3.805A pdb=" N VAL K 27 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16 496 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 7.81 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: 3591 1.34 - 1.46: 4442 1.46 - 1.58: 6804 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" CB GLU K 25 " pdb=" CG GLU K 25 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CB MET D 59 " pdb=" CG MET D 59 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.17e-01 bond pdb=" C4' DA I -35 " pdb=" C3' DA I -35 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 8.82e-01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.64: 1535 105.64 - 112.76: 8634 112.76 - 119.87: 5353 119.87 - 126.99: 5910 126.99 - 134.10: 739 Bond angle restraints: 22171 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.94e+00 angle pdb=" CA ARG L 125 " pdb=" CB ARG L 125 " pdb=" CG ARG L 125 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.88e+00 angle pdb=" C ASN L 135 " pdb=" N ARG L 136 " pdb=" CA ARG L 136 " ideal model delta sigma weight residual 121.14 116.17 4.97 1.75e+00 3.27e-01 8.08e+00 angle pdb=" CB GLU K 25 " pdb=" CG GLU K 25 " pdb=" CD GLU K 25 " ideal model delta sigma weight residual 112.60 117.37 -4.77 1.70e+00 3.46e-01 7.86e+00 angle pdb=" C PHE L 62 " pdb=" N LYS L 63 " pdb=" CA LYS L 63 " ideal model delta sigma weight residual 122.74 129.55 -6.81 2.44e+00 1.68e-01 7.78e+00 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 7234 35.23 - 70.47: 1346 70.47 - 105.70: 23 105.70 - 140.94: 0 140.94 - 176.17: 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 36.17 -176.17 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 71.38 148.62 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CB GLU G 56 " pdb=" CG GLU G 56 " pdb=" CD GLU G 56 " pdb=" OE1 GLU G 56 " ideal model delta sinusoidal sigma weight residual 0.00 -88.89 88.89 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1770 0.032 - 0.064: 575 0.064 - 0.096: 112 0.096 - 0.128: 53 0.128 - 0.160: 6 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA ARG L 125 " pdb=" N ARG L 125 " pdb=" C ARG L 125 " pdb=" CB ARG L 125 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA LYS L 101 " pdb=" N LYS L 101 " pdb=" C LYS L 101 " pdb=" CB LYS L 101 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 2513 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU K 25 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C GLU K 25 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU K 25 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO K 26 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.024 2.00e-02 2.50e+03 1.02e-02 2.84e+00 pdb=" N9 DA I -35 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.000 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 33 " 0.009 2.00e-02 2.50e+03 1.02e-02 2.60e+00 pdb=" CG TRP L 33 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP L 33 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP L 33 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP L 33 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 33 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 33 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP L 33 " 0.001 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1945 2.76 - 3.47: 19659 3.47 - 4.19: 38406 4.19 - 4.90: 59651 Nonbonded interactions: 119663 Sorted by model distance: nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.329 3.350 nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.331 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.084 2.496 nonbonded pdb=" O ARG L 125 " pdb=" OG1 THR L 129 " model vdw 2.135 2.440 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.161 2.440 ... (remaining 119658 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: 1.150 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: 0.010 Extract box with map and model: 4.200 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 49.300 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.004 0.041 15472 Z= 0.217 Angle : 0.566 7.352 22171 Z= 0.327 Chirality : 0.035 0.160 2516 Planarity : 0.004 0.038 1794 Dihedral : 25.930 176.171 6577 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.68 % 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: 1.99 (0.26), residues: 1057 helix: 2.41 (0.21), residues: 626 sheet: 1.10 (0.75), residues: 50 loop : -0.53 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 33 HIS 0.002 0.001 HIS K 65 PHE 0.015 0.001 PHE L 56 TYR 0.018 0.001 TYR H 83 ARG 0.006 0.000 ARG K 68 *********************** 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 243 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 0.983 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: A 81 ASP cc_start: 0.8084 (m-30) cc_final: 0.7869 (m-30) REVERT: A 94 GLU cc_start: 0.8400 (tp30) cc_final: 0.7955 (mm-30) REVERT: C 75 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8550 (mttm) REVERT: C 95 LYS cc_start: 0.8850 (tptt) cc_final: 0.8643 (tptm) REVERT: D 33 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7873 (mtp-110) REVERT: D 86 ARG cc_start: 0.8743 (mmt-90) cc_final: 0.8382 (mmt90) REVERT: H 100 LEU cc_start: 0.9442 (mt) cc_final: 0.9172 (mp) REVERT: K 42 SER cc_start: 0.7939 (p) cc_final: 0.7269 (p) REVERT: K 66 THR cc_start: 0.7827 (m) cc_final: 0.7608 (m) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3419 time to fit residues: 112.1259 Evaluate side-chains 199 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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: 9.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 32 HIS M 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15472 Z= 0.209 Angle : 0.580 10.950 22171 Z= 0.330 Chirality : 0.035 0.262 2516 Planarity : 0.004 0.038 1794 Dihedral : 28.807 176.496 4413 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.62 % Allowed : 10.28 % Favored : 88.10 % 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: 2.43 (0.21), residues: 647 sheet: 0.99 (0.71), residues: 55 loop : -0.63 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 33 HIS 0.004 0.001 HIS L 75 PHE 0.031 0.002 PHE L 62 TYR 0.026 0.002 TYR H 83 ARG 0.006 0.000 ARG H 33 *********************** 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 220 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 1.107 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: C 95 LYS cc_start: 0.8887 (tptt) cc_final: 0.8640 (tptm) REVERT: D 33 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7665 (mtp-110) REVERT: D 86 ARG cc_start: 0.8690 (mmt-90) cc_final: 0.8304 (mmt90) REVERT: E 125 GLN cc_start: 0.8356 (mt0) cc_final: 0.8122 (mp10) REVERT: H 100 LEU cc_start: 0.9452 (mt) cc_final: 0.9167 (mp) REVERT: K 66 THR cc_start: 0.8086 (m) cc_final: 0.7777 (m) REVERT: K 68 ARG cc_start: 0.7280 (ptp90) cc_final: 0.6752 (mtm180) REVERT: L 74 TYR cc_start: 0.8147 (t80) cc_final: 0.7859 (t80) outliers start: 14 outliers final: 11 residues processed: 212 average time/residue: 0.3230 time to fit residues: 93.8549 Evaluate side-chains 199 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15472 Z= 0.370 Angle : 0.634 9.330 22171 Z= 0.360 Chirality : 0.039 0.159 2516 Planarity : 0.004 0.041 1794 Dihedral : 28.935 174.398 4413 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.16 % Allowed : 13.96 % Favored : 83.87 % 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: 1.64 (0.26), residues: 1057 helix: 2.15 (0.20), residues: 647 sheet: 0.95 (0.72), residues: 50 loop : -0.92 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 33 HIS 0.008 0.001 HIS L 0 PHE 0.014 0.002 PHE L 62 TYR 0.033 0.002 TYR H 83 ARG 0.006 0.001 ARG H 33 *********************** 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 227 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 1.188 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: C 95 LYS cc_start: 0.8976 (tptt) cc_final: 0.8619 (tptm) REVERT: D 33 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7668 (mtp-110) REVERT: D 86 ARG cc_start: 0.8777 (mmt-90) cc_final: 0.8369 (mmt90) REVERT: H 59 MET cc_start: 0.8715 (tpp) cc_final: 0.8325 (tpt) REVERT: K 42 SER cc_start: 0.7352 (p) cc_final: 0.7073 (p) REVERT: L 60 TYR cc_start: 0.8324 (t80) cc_final: 0.8123 (t80) REVERT: L 74 TYR cc_start: 0.8171 (t80) cc_final: 0.7954 (t80) REVERT: L 75 HIS cc_start: 0.8583 (t-90) cc_final: 0.8374 (t-90) outliers start: 20 outliers final: 16 residues processed: 218 average time/residue: 0.3290 time to fit residues: 97.3932 Evaluate side-chains 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain L residue 45 TYR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15472 Z= 0.224 Angle : 0.583 10.523 22171 Z= 0.332 Chirality : 0.036 0.308 2516 Planarity : 0.004 0.039 1794 Dihedral : 28.792 176.353 4413 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.49 % Allowed : 16.02 % Favored : 81.49 % 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: 1.89 (0.26), residues: 1057 helix: 2.34 (0.21), residues: 646 sheet: 0.93 (0.73), residues: 50 loop : -0.75 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 33 HIS 0.003 0.001 HIS B 75 PHE 0.016 0.001 PHE L 62 TYR 0.021 0.002 TYR H 83 ARG 0.007 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 224 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8456 (mmtp) cc_final: 0.8233 (mmtm) REVERT: C 73 ASN cc_start: 0.8254 (t0) cc_final: 0.7988 (t0) REVERT: C 95 LYS cc_start: 0.8959 (tptt) cc_final: 0.8648 (tptm) REVERT: D 33 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7590 (mtp-110) REVERT: D 86 ARG cc_start: 0.8720 (mmt-90) cc_final: 0.8336 (mmt90) REVERT: E 94 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7671 (mm-30) REVERT: L 8 LYS cc_start: 0.8588 (mppt) cc_final: 0.8331 (tptp) REVERT: L 134 TYR cc_start: 0.6366 (t80) cc_final: 0.5693 (t80) outliers start: 23 outliers final: 17 residues processed: 212 average time/residue: 0.3339 time to fit residues: 96.1669 Evaluate side-chains 209 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain L residue 45 TYR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15472 Z= 0.312 Angle : 0.615 11.421 22171 Z= 0.347 Chirality : 0.037 0.266 2516 Planarity : 0.004 0.040 1794 Dihedral : 28.882 175.330 4413 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.71 % Allowed : 17.21 % Favored : 80.09 % 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: 1.69 (0.26), residues: 1057 helix: 2.19 (0.21), residues: 646 sheet: 0.87 (0.71), residues: 50 loop : -0.88 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 93 HIS 0.003 0.001 HIS H 49 PHE 0.013 0.002 PHE L 62 TYR 0.023 0.002 TYR L 134 ARG 0.009 0.001 ARG L 90 *********************** 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 225 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8250 (t0) cc_final: 0.7975 (t0) REVERT: C 95 LYS cc_start: 0.9011 (tptt) cc_final: 0.8695 (tptm) REVERT: D 86 ARG cc_start: 0.8757 (mmt-90) cc_final: 0.8354 (mmt90) REVERT: E 94 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 59 MET cc_start: 0.8634 (tpp) cc_final: 0.8234 (tpt) REVERT: H 119 THR cc_start: 0.9457 (t) cc_final: 0.9225 (t) REVERT: L 8 LYS cc_start: 0.8595 (mppt) cc_final: 0.8342 (tptp) REVERT: L 75 HIS cc_start: 0.8363 (t-90) cc_final: 0.8099 (t-90) outliers start: 25 outliers final: 19 residues processed: 213 average time/residue: 0.3374 time to fit residues: 97.2937 Evaluate side-chains 214 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 45 TYR Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.5980 chunk 112 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15472 Z= 0.186 Angle : 0.579 12.652 22171 Z= 0.327 Chirality : 0.035 0.298 2516 Planarity : 0.004 0.052 1794 Dihedral : 28.759 176.943 4413 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.06 % Allowed : 18.40 % Favored : 79.55 % 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: 2.42 (0.21), residues: 646 sheet: 0.95 (0.71), residues: 50 loop : -0.78 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 93 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.001 PHE L 62 TYR 0.016 0.001 TYR F 88 ARG 0.010 0.000 ARG L 90 *********************** 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 222 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8215 (t) REVERT: C 73 ASN cc_start: 0.8205 (t0) cc_final: 0.7977 (t0) REVERT: C 95 LYS cc_start: 0.8941 (tptt) cc_final: 0.8634 (tptm) REVERT: D 86 ARG cc_start: 0.8643 (mmt-90) cc_final: 0.8255 (mmt90) REVERT: H 119 THR cc_start: 0.9445 (t) cc_final: 0.9219 (t) REVERT: L 9 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7423 (mm-30) REVERT: L 69 PHE cc_start: 0.7445 (m-80) cc_final: 0.7189 (m-80) outliers start: 19 outliers final: 14 residues processed: 214 average time/residue: 0.3398 time to fit residues: 98.7435 Evaluate side-chains 212 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15472 Z= 0.212 Angle : 0.593 13.443 22171 Z= 0.332 Chirality : 0.036 0.315 2516 Planarity : 0.004 0.045 1794 Dihedral : 28.762 176.528 4413 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.06 % Allowed : 18.83 % Favored : 79.11 % 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: 1.94 (0.26), residues: 1057 helix: 2.40 (0.21), residues: 646 sheet: 1.02 (0.72), residues: 50 loop : -0.80 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 93 HIS 0.005 0.001 HIS L 75 PHE 0.012 0.001 PHE L 62 TYR 0.034 0.002 TYR L 60 ARG 0.012 0.001 ARG L 90 *********************** 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 219 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8194 (t) REVERT: C 73 ASN cc_start: 0.8197 (t0) cc_final: 0.7975 (t0) REVERT: C 95 LYS cc_start: 0.8936 (tptt) cc_final: 0.8639 (tptm) REVERT: D 86 ARG cc_start: 0.8660 (mmt-90) cc_final: 0.8257 (mmt90) REVERT: E 125 GLN cc_start: 0.8531 (mt0) cc_final: 0.8143 (mp10) REVERT: H 119 THR cc_start: 0.9456 (t) cc_final: 0.9231 (t) REVERT: L 69 PHE cc_start: 0.7627 (m-80) cc_final: 0.7386 (m-80) REVERT: L 75 HIS cc_start: 0.8073 (t-90) cc_final: 0.7707 (t-90) outliers start: 19 outliers final: 16 residues processed: 212 average time/residue: 0.3354 time to fit residues: 96.5211 Evaluate side-chains 215 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 0.0270 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15472 Z= 0.230 Angle : 0.610 13.624 22171 Z= 0.339 Chirality : 0.036 0.312 2516 Planarity : 0.004 0.042 1794 Dihedral : 28.781 176.491 4413 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.38 % Allowed : 19.26 % Favored : 78.35 % 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: 1.94 (0.26), residues: 1057 helix: 2.40 (0.21), residues: 646 sheet: 1.23 (0.75), residues: 50 loop : -0.84 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 33 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE L 62 TYR 0.043 0.002 TYR L 134 ARG 0.012 0.001 ARG L 90 *********************** 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 222 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8180 (t) REVERT: C 73 ASN cc_start: 0.8203 (t0) cc_final: 0.7972 (t0) REVERT: C 95 LYS cc_start: 0.8948 (tptt) cc_final: 0.8647 (tptm) REVERT: D 86 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8180 (mmt90) REVERT: E 125 GLN cc_start: 0.8533 (mt0) cc_final: 0.8126 (mp10) REVERT: H 119 THR cc_start: 0.9465 (t) cc_final: 0.9244 (t) REVERT: L 9 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7650 (mm-30) REVERT: L 69 PHE cc_start: 0.7638 (m-80) cc_final: 0.7371 (m-80) REVERT: L 75 HIS cc_start: 0.8171 (t-90) cc_final: 0.7848 (t-90) outliers start: 22 outliers final: 17 residues processed: 213 average time/residue: 0.3286 time to fit residues: 95.1489 Evaluate side-chains 215 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 134 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 0.0030 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15472 Z= 0.230 Angle : 0.620 13.956 22171 Z= 0.343 Chirality : 0.036 0.313 2516 Planarity : 0.004 0.047 1794 Dihedral : 28.791 176.385 4413 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.06 % Allowed : 20.45 % Favored : 77.49 % 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: 1.94 (0.26), residues: 1057 helix: 2.39 (0.21), residues: 646 sheet: 1.32 (0.75), residues: 50 loop : -0.83 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 33 HIS 0.003 0.001 HIS L 55 PHE 0.014 0.001 PHE L 62 TYR 0.038 0.002 TYR L 134 ARG 0.014 0.001 ARG L 90 *********************** 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 220 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 ARG cc_start: 0.7970 (mmt-90) cc_final: 0.7672 (mpt180) REVERT: C 16 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8178 (t) REVERT: C 73 ASN cc_start: 0.8216 (t0) cc_final: 0.7984 (t0) REVERT: C 95 LYS cc_start: 0.8946 (tptt) cc_final: 0.8647 (tptm) REVERT: D 86 ARG cc_start: 0.8600 (mmt-90) cc_final: 0.8183 (mmt90) REVERT: E 94 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7838 (mm-30) REVERT: E 125 GLN cc_start: 0.8516 (mt0) cc_final: 0.8124 (mt0) REVERT: G 13 LYS cc_start: 0.8469 (tppp) cc_final: 0.8163 (mmmt) REVERT: H 119 THR cc_start: 0.9453 (t) cc_final: 0.9234 (t) REVERT: L 69 PHE cc_start: 0.7631 (m-80) cc_final: 0.7365 (m-80) REVERT: L 75 HIS cc_start: 0.8186 (t-90) cc_final: 0.7792 (t-90) outliers start: 19 outliers final: 16 residues processed: 213 average time/residue: 0.3222 time to fit residues: 93.4866 Evaluate side-chains 212 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 0.0770 chunk 102 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 0.3980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15472 Z= 0.191 Angle : 0.618 15.749 22171 Z= 0.343 Chirality : 0.036 0.321 2516 Planarity : 0.004 0.047 1794 Dihedral : 28.739 176.962 4413 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 20.67 % Favored : 77.27 % 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: 2.03 (0.26), residues: 1057 helix: 2.40 (0.21), residues: 650 sheet: 1.32 (0.75), residues: 50 loop : -0.68 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 33 HIS 0.005 0.001 HIS H 82 PHE 0.011 0.001 PHE L 62 TYR 0.039 0.002 TYR F 88 ARG 0.013 0.000 ARG L 90 ********************** 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 220 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 ARG cc_start: 0.7942 (mmt-90) cc_final: 0.7656 (mpt180) REVERT: C 16 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8133 (t) REVERT: C 73 ASN cc_start: 0.8215 (t0) cc_final: 0.7998 (t0) REVERT: C 95 LYS cc_start: 0.8916 (tptt) cc_final: 0.8621 (tptm) REVERT: E 94 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7798 (mm-30) REVERT: E 125 GLN cc_start: 0.8493 (mt0) cc_final: 0.8079 (mt0) REVERT: H 119 THR cc_start: 0.9463 (t) cc_final: 0.9236 (t) REVERT: L 9 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7525 (mp0) REVERT: L 69 PHE cc_start: 0.7596 (m-80) cc_final: 0.7327 (m-80) REVERT: L 75 HIS cc_start: 0.8058 (t-90) cc_final: 0.7791 (t-90) REVERT: L 97 LEU cc_start: 0.8489 (tp) cc_final: 0.8279 (tt) outliers start: 19 outliers final: 17 residues processed: 213 average time/residue: 0.3313 time to fit residues: 96.7173 Evaluate side-chains 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087078 restraints weight = 41325.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087015 restraints weight = 32971.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.087757 restraints weight = 27010.743| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15472 Z= 0.245 Angle : 0.628 15.493 22171 Z= 0.348 Chirality : 0.037 0.309 2516 Planarity : 0.004 0.051 1794 Dihedral : 28.807 176.208 4413 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.95 % Allowed : 21.10 % Favored : 76.95 % 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: 1.94 (0.26), residues: 1057 helix: 2.32 (0.21), residues: 650 sheet: 1.59 (0.76), residues: 48 loop : -0.73 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 93 HIS 0.008 0.001 HIS L 0 PHE 0.011 0.001 PHE L 62 TYR 0.040 0.002 TYR H 83 ARG 0.013 0.001 ARG L 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.35 seconds wall clock time: 48 minutes 1.74 seconds (2881.74 seconds total)