Starting phenix.real_space_refine on Mon Apr 8 21:32:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/04_2024/8sn7_40615.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/04_2024/8sn7_40615.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/8sn7_40615/04_2024/8sn7_40615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/04_2024/8sn7_40615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/04_2024/8sn7_40615.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/04_2024/8sn7_40615.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 TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "G GLU -57": "OE1" <-> "OE2" Residue "G ASP -41": "OD1" <-> "OD2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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 33.174 72.290 48.380 1.00 72.35 S ATOM 12446 SG CYS K 51 31.114 69.178 47.704 1.00 73.71 S ATOM 12470 SG CYS K 54 32.901 70.989 44.890 1.00 79.16 S ATOM 12187 SG CYS K 16 22.600 66.502 53.978 1.00 79.23 S ATOM 12205 SG CYS K 19 20.009 64.339 55.691 1.00 76.33 S ATOM 12335 SG CYS K 36 23.168 65.453 57.650 1.00 74.99 S ATOM 12357 SG CYS K 39 23.514 62.918 55.146 1.00 76.41 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: 7.76, per 1000 atoms: 0.53 Number of scatterers: 14600 At special positions: 0 Unit cell: (110.224, 131.472, 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: 7.02 Conformation dependent library (CDL) restraints added in 2.0 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 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " 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 " 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: 47 helices and 12 sheets defined 62.9% alpha, 4.5% beta 136 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.543A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (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: 3.683A 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: 3.919A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.675A 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 129 through 134 removed outlier: 3.864A pdb=" N ALA C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 150 Processing helix chain 'C' and resid 159 through 186 removed outlier: 3.548A pdb=" N LEU C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.795A 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: 3.602A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.697A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (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 removed outlier: 4.006A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.833A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.635A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid -97 through -92 Processing helix chain 'G' and resid -86 through -76 Processing helix chain 'G' and resid -67 through -40 Processing helix chain 'G' and resid -34 through -23 removed outlier: 3.658A pdb=" N ASP G -23 " --> pdb=" O ALA G -27 " (cutoff:3.500A) Processing helix chain 'G' and resid -22 through -16 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.549A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.650A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.730A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 15 removed outlier: 3.895A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.861A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.025A 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 90 removed outlier: 3.567A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.676A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.132A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.575A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 143 removed outlier: 3.968A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 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: 7.099A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 155 through 156 removed outlier: 8.078A pdb=" N ARG C 155 " --> 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 190 through 191 Processing sheet with id=AA6, first strand: chain 'C' and resid 214 through 215 removed outlier: 7.013A pdb=" N THR C 214 " --> 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: 7.205A 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 -71 through -70 removed outlier: 7.725A pdb=" N ARG G -71 " --> 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 'K' and resid 27 through 28 removed outlier: 3.558A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB3, first strand: chain 'M' and resid 5 through 6 491 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3222 1.33 - 1.45: 4431 1.45 - 1.57: 7184 1.57 - 1.69: 586 1.69 - 1.81: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" CG LEU M 50 " pdb=" CD1 LEU M 50 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.08e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CB GLU C 174 " pdb=" CG GLU C 174 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 1.02e+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 1.02e+00 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.64: 1540 105.64 - 112.72: 8608 112.72 - 119.81: 5211 119.81 - 126.89: 5989 126.89 - 133.97: 823 Bond angle restraints: 22171 Sorted by residual: angle pdb=" C CYS K 31 " pdb=" N ASN K 32 " pdb=" CA ASN K 32 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C3' DG J -70 " pdb=" C2' DG J -70 " pdb=" C1' DG J -70 " ideal model delta sigma weight residual 101.60 105.65 -4.05 1.50e+00 4.44e-01 7.31e+00 angle pdb=" CB MET L 38 " pdb=" CG MET L 38 " pdb=" SD MET L 38 " ideal model delta sigma weight residual 112.70 120.02 -7.32 3.00e+00 1.11e-01 5.95e+00 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 125.89 -3.43 1.41e+00 5.03e-01 5.93e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 105.40 7.30 3.00e+00 1.11e-01 5.92e+00 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 7270 35.74 - 71.48: 1318 71.48 - 107.22: 15 107.22 - 142.96: 0 142.96 - 178.70: 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 220.00 41.30 178.70 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 70.18 149.82 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CB GLU D 105 " pdb=" CG GLU D 105 " pdb=" CD GLU D 105 " pdb=" OE1 GLU D 105 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1777 0.032 - 0.065: 559 0.065 - 0.097: 128 0.097 - 0.129: 46 0.129 - 0.162: 6 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CG LEU F 62 " pdb=" CB LEU F 62 " pdb=" CD1 LEU F 62 " pdb=" CD2 LEU F 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ASN K 32 " pdb=" N ASN K 32 " pdb=" C ASN K 32 " pdb=" CB ASN K 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 2513 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 60 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO L 61 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO K 38 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.027 2.00e-02 2.50e+03 1.15e-02 3.66e+00 pdb=" N9 DA I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.002 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 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1940 2.76 - 3.47: 19329 3.47 - 4.19: 38549 4.19 - 4.90: 60082 Nonbonded interactions: 119902 Sorted by model distance: nonbonded pdb=" N SER G-102 " pdb=" C SER H 123 " model vdw 1.330 3.350 nonbonded pdb=" N SER C 124 " pdb=" C SER D 123 " model vdw 1.330 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.210 2.496 nonbonded pdb=" N SER C 124 " pdb=" O SER D 123 " model vdw 2.250 2.520 nonbonded pdb=" N SER G-102 " pdb=" O SER H 123 " model vdw 2.252 2.520 ... (remaining 119897 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 -102 through 5) } 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=0.00 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: 1.100 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: 4.190 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 48.620 Find NCS groups from input model: 0.630 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 0.048 15472 Z= 0.212 Angle : 0.567 7.799 22171 Z= 0.329 Chirality : 0.035 0.162 2516 Planarity : 0.004 0.073 1794 Dihedral : 25.759 178.704 6577 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 1.83 (0.26), residues: 1057 helix: 2.34 (0.21), residues: 627 sheet: -1.13 (0.72), residues: 41 loop : -0.41 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 77 HIS 0.004 0.001 HIS D 82 PHE 0.008 0.001 PHE E 78 TYR 0.025 0.002 TYR M 59 ARG 0.005 0.000 ARG L 125 *********************** 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 222 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8564 (ttmm) REVERT: E 76 GLN cc_start: 0.8261 (pp30) cc_final: 0.8002 (pp30) REVERT: H 34 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8899 (mtmm) REVERT: H 86 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7804 (mmt-90) REVERT: H 120 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8569 (ttpp) REVERT: L 63 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8253 (mttt) REVERT: L 114 ASN cc_start: 0.7881 (t0) cc_final: 0.7667 (m-40) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.3350 time to fit residues: 102.4541 Evaluate side-chains 189 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0848 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= 0.262 Angle : 0.595 10.452 22171 Z= 0.340 Chirality : 0.036 0.162 2516 Planarity : 0.005 0.050 1794 Dihedral : 28.871 179.651 4413 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.30 % Allowed : 10.39 % Favored : 88.31 % 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: 1.73 (0.27), residues: 1057 helix: 2.30 (0.21), residues: 649 sheet: -1.53 (0.76), residues: 37 loop : -0.67 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.012 0.001 PHE L 62 TYR 0.026 0.002 TYR L 134 ARG 0.011 0.000 ARG H 92 *********************** 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 204 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 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: symmetry clash REVERT: E 76 GLN cc_start: 0.8268 (pp30) cc_final: 0.7958 (pp30) REVERT: E 120 MET cc_start: 0.8389 (mtp) cc_final: 0.8148 (mtt) REVERT: H 34 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8870 (mtmm) REVERT: H 86 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7813 (mmt-90) REVERT: H 120 LYS cc_start: 0.9107 (ttpt) cc_final: 0.8667 (ttpt) REVERT: L 63 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8376 (mttt) REVERT: L 127 TYR cc_start: 0.7808 (t80) cc_final: 0.7357 (t80) REVERT: L 133 LYS cc_start: 0.7634 (mmmt) cc_final: 0.7138 (mmmt) REVERT: L 136 ARG cc_start: 0.8474 (pmt-80) cc_final: 0.8111 (pmt-80) outliers start: 12 outliers final: 9 residues processed: 196 average time/residue: 0.3287 time to fit residues: 88.3706 Evaluate side-chains 195 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain M residue 13 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 104 optimal weight: 0.0050 chunk 116 optimal weight: 0.0070 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 92 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15472 Z= 0.325 Angle : 0.614 10.328 22171 Z= 0.352 Chirality : 0.038 0.162 2516 Planarity : 0.005 0.050 1794 Dihedral : 29.133 179.455 4413 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.27 % Allowed : 13.42 % Favored : 84.31 % 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: 1.57 (0.27), residues: 1057 helix: 2.17 (0.21), residues: 652 sheet: -1.65 (0.74), residues: 33 loop : -0.76 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.012 0.002 PHE G -88 TYR 0.022 0.002 TYR A 54 ARG 0.005 0.001 ARG A 128 *********************** 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 206 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.169 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: E 94 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8591 (mm-30) REVERT: H 86 ARG cc_start: 0.8159 (mmt90) cc_final: 0.7845 (mmt-90) REVERT: H 120 LYS cc_start: 0.9129 (ttpt) cc_final: 0.8679 (ttpt) outliers start: 21 outliers final: 16 residues processed: 196 average time/residue: 0.3444 time to fit residues: 93.1575 Evaluate side-chains 195 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue -94 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain M residue 13 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 0.0040 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 92 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15472 Z= 0.196 Angle : 0.566 9.941 22171 Z= 0.326 Chirality : 0.035 0.259 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.082 179.945 4413 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 14.83 % Favored : 83.12 % 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: 1.81 (0.27), residues: 1057 helix: 2.37 (0.21), residues: 652 sheet: -1.66 (0.73), residues: 33 loop : -0.69 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.016 0.001 PHE L 51 TYR 0.023 0.002 TYR D 83 ARG 0.005 0.000 ARG H 92 *********************** 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 206 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 1.199 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: E 94 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8477 (mm-30) REVERT: H 86 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7783 (mmt-90) REVERT: H 120 LYS cc_start: 0.9171 (ttpt) cc_final: 0.8723 (ttpt) REVERT: L 72 ARG cc_start: 0.7349 (ttt180) cc_final: 0.7104 (ttt90) REVERT: L 147 MET cc_start: 0.6627 (mpp) cc_final: 0.6185 (mpp) outliers start: 19 outliers final: 14 residues processed: 195 average time/residue: 0.3215 time to fit residues: 86.3966 Evaluate side-chains 198 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain M residue 13 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 92 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1544 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= 0.243 Angle : 0.593 10.253 22171 Z= 0.337 Chirality : 0.036 0.237 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.152 179.270 4413 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.06 % Allowed : 16.13 % Favored : 81.82 % 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: 1.76 (0.27), residues: 1057 helix: 2.33 (0.21), residues: 653 sheet: -1.61 (0.75), residues: 33 loop : -0.71 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.012 0.002 PHE L 51 TYR 0.019 0.002 TYR H 83 ARG 0.006 0.000 ARG L 136 *********************** 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 201 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 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: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8515 (mm-30) REVERT: H 86 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7804 (mmt-90) REVERT: H 120 LYS cc_start: 0.9171 (ttpt) cc_final: 0.8712 (ttpt) REVERT: L 72 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6810 (ttt90) REVERT: L 73 ILE cc_start: 0.7713 (mp) cc_final: 0.7398 (tp) REVERT: L 147 MET cc_start: 0.6989 (mpp) cc_final: 0.6529 (mpp) outliers start: 19 outliers final: 16 residues processed: 190 average time/residue: 0.3168 time to fit residues: 83.2249 Evaluate side-chains 195 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 144 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 0.0020 chunk 120 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15472 Z= 0.187 Angle : 0.568 10.856 22171 Z= 0.324 Chirality : 0.035 0.223 2516 Planarity : 0.004 0.047 1794 Dihedral : 29.121 179.326 4413 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.95 % Allowed : 16.56 % 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: 1.90 (0.27), residues: 1057 helix: 2.43 (0.21), residues: 653 sheet: -1.53 (0.74), residues: 33 loop : -0.64 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 141 HIS 0.003 0.001 HIS E 39 PHE 0.014 0.001 PHE L 62 TYR 0.015 0.001 TYR K 64 ARG 0.008 0.000 ARG L 125 *********************** 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 204 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8507 (pm20) cc_final: 0.7497 (pm20) REVERT: E 94 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8453 (mm-30) REVERT: H 86 ARG cc_start: 0.8057 (mmt90) cc_final: 0.7772 (mmt-90) REVERT: H 120 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8715 (ttpt) REVERT: L 147 MET cc_start: 0.6753 (mpp) cc_final: 0.6295 (mpp) outliers start: 18 outliers final: 15 residues processed: 195 average time/residue: 0.3090 time to fit residues: 84.7249 Evaluate side-chains 194 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 144 LYS 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: 0.5980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 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: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1759 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= 0.205 Angle : 0.575 10.718 22171 Z= 0.327 Chirality : 0.035 0.224 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.152 179.199 4413 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.16 % Allowed : 17.10 % Favored : 80.74 % 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: 1.90 (0.27), residues: 1057 helix: 2.44 (0.21), residues: 653 sheet: -1.40 (0.76), residues: 33 loop : -0.69 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 141 HIS 0.004 0.001 HIS D 82 PHE 0.022 0.002 PHE L 62 TYR 0.015 0.002 TYR D 83 ARG 0.006 0.000 ARG L 125 *********************** 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 204 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8462 (mm-30) REVERT: G -100 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7528 (mmtm) REVERT: H 86 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7777 (mmt-90) REVERT: H 120 LYS cc_start: 0.9155 (ttpt) cc_final: 0.8717 (ttpt) REVERT: K 42 SER cc_start: 0.7514 (p) cc_final: 0.7249 (p) REVERT: L 5 ARG cc_start: 0.8243 (ttt-90) cc_final: 0.7988 (ttt-90) REVERT: L 72 ARG cc_start: 0.7257 (ttt180) cc_final: 0.6909 (ttt90) REVERT: L 73 ILE cc_start: 0.7810 (mp) cc_final: 0.7369 (tp) REVERT: L 147 MET cc_start: 0.6871 (mpp) cc_final: 0.6388 (mpp) outliers start: 20 outliers final: 15 residues processed: 194 average time/residue: 0.3066 time to fit residues: 83.3151 Evaluate side-chains 197 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 144 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.6980 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: 5.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15472 Z= 0.314 Angle : 0.622 11.352 22171 Z= 0.351 Chirality : 0.037 0.242 2516 Planarity : 0.004 0.047 1794 Dihedral : 29.336 178.573 4413 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.06 % Allowed : 17.86 % 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: 1.77 (0.26), residues: 1057 helix: 2.31 (0.21), residues: 653 sheet: -0.62 (0.95), residues: 23 loop : -0.76 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 141 HIS 0.004 0.001 HIS E 39 PHE 0.022 0.002 PHE L 62 TYR 0.028 0.002 TYR L 134 ARG 0.007 0.000 ARG L 125 *********************** 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 199 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8535 (pm20) cc_final: 0.7529 (pm20) REVERT: B 84 MET cc_start: 0.8505 (tpp) cc_final: 0.8279 (mmm) REVERT: E 61 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8914 (mm) REVERT: E 94 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8585 (mm-30) REVERT: G -100 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7901 (mmtm) REVERT: H 86 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7817 (mmt-90) REVERT: H 120 LYS cc_start: 0.9129 (ttpt) cc_final: 0.8682 (ttpt) REVERT: L 5 ARG cc_start: 0.8187 (ttt-90) cc_final: 0.7897 (ttt-90) REVERT: L 72 ARG cc_start: 0.7495 (ttt180) cc_final: 0.7145 (ttt-90) REVERT: L 73 ILE cc_start: 0.7713 (mp) cc_final: 0.7280 (tp) REVERT: L 147 MET cc_start: 0.7258 (mpp) cc_final: 0.6859 (mpp) outliers start: 19 outliers final: 16 residues processed: 189 average time/residue: 0.3255 time to fit residues: 84.8647 Evaluate side-chains 194 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1989 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= 0.243 Angle : 0.603 11.405 22171 Z= 0.341 Chirality : 0.036 0.223 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.309 179.044 4413 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.73 % Allowed : 18.83 % Favored : 79.44 % 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: 1.79 (0.26), residues: 1057 helix: 2.34 (0.21), residues: 653 sheet: -1.17 (0.82), residues: 23 loop : -0.75 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 141 HIS 0.004 0.001 HIS E 39 PHE 0.016 0.002 PHE L 50 TYR 0.024 0.002 TYR L 134 ARG 0.015 0.000 ARG L 125 *********************** 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 196 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8534 (pm20) cc_final: 0.7538 (pm20) REVERT: E 61 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8949 (mm) REVERT: E 94 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8544 (mm-30) REVERT: H 86 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7799 (mmt-90) REVERT: H 120 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8687 (ttpt) REVERT: L 72 ARG cc_start: 0.7605 (ttt180) cc_final: 0.7222 (ttt-90) REVERT: L 73 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7358 (tp) REVERT: L 147 MET cc_start: 0.7178 (mpp) cc_final: 0.6772 (mpp) outliers start: 16 outliers final: 14 residues processed: 189 average time/residue: 0.3150 time to fit residues: 83.1351 Evaluate side-chains 192 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN 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: 7.9990 chunk 128 optimal weight: 5.9990 chunk 118 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.0030 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15472 Z= 0.185 Angle : 0.593 12.656 22171 Z= 0.335 Chirality : 0.035 0.215 2516 Planarity : 0.004 0.047 1794 Dihedral : 29.212 179.245 4413 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.84 % Allowed : 18.72 % Favored : 79.44 % 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: 1.83 (0.27), residues: 1057 helix: 2.45 (0.21), residues: 652 sheet: -1.64 (0.60), residues: 48 loop : -0.75 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 141 HIS 0.003 0.001 HIS E 39 PHE 0.014 0.001 PHE L 62 TYR 0.026 0.002 TYR L 134 ARG 0.011 0.000 ARG L 125 ********************** 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 201 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.148 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 59 GLU cc_start: 0.8512 (pm20) cc_final: 0.7524 (pm20) REVERT: E 61 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8927 (mm) REVERT: E 94 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8467 (mm-30) REVERT: H 86 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7768 (mmt-90) REVERT: H 120 LYS cc_start: 0.9153 (ttpt) cc_final: 0.8718 (ttpt) REVERT: L 72 ARG cc_start: 0.7607 (ttt180) cc_final: 0.7275 (ttt-90) REVERT: L 73 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7303 (tp) outliers start: 17 outliers final: 14 residues processed: 193 average time/residue: 0.3148 time to fit residues: 85.3933 Evaluate side-chains 196 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 144 LYS 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: 0.9980 chunk 28 optimal weight: 0.4980 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092108 restraints weight = 37852.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091690 restraints weight = 33145.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.093099 restraints weight = 25578.329| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15472 Z= 0.190 Angle : 0.591 10.525 22171 Z= 0.334 Chirality : 0.035 0.215 2516 Planarity : 0.004 0.047 1794 Dihedral : 29.195 179.071 4413 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.62 % Allowed : 19.37 % Favored : 79.00 % 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: 1.82 (0.27), residues: 1057 helix: 2.43 (0.21), residues: 652 sheet: -1.62 (0.61), residues: 48 loop : -0.74 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 141 HIS 0.003 0.001 HIS E 39 PHE 0.026 0.001 PHE L 62 TYR 0.026 0.001 TYR L 134 ARG 0.010 0.000 ARG L 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.82 seconds wall clock time: 48 minutes 33.01 seconds (2913.01 seconds total)