Starting phenix.real_space_refine on Mon Apr 8 21:31:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/04_2024/8sn4_40612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/04_2024/8sn4_40612.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/8sn4_40612/04_2024/8sn4_40612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/04_2024/8sn4_40612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/04_2024/8sn4_40612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/04_2024/8sn4_40612.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 "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 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 33.347 72.273 47.031 1.00 86.22 S ATOM 12446 SG CYS K 51 34.177 68.839 45.573 1.00 81.44 S ATOM 12470 SG CYS K 54 33.180 71.557 43.284 1.00 91.27 S ATOM 12187 SG CYS K 16 23.217 66.833 52.909 1.00107.40 S ATOM 12205 SG CYS K 19 21.018 64.361 54.707 1.00109.20 S ATOM 12335 SG CYS K 36 24.056 65.730 56.569 1.00 99.38 S ATOM 12357 SG CYS K 39 24.585 63.331 53.903 1.00 91.82 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 8.47, per 1000 atoms: 0.58 Number of scatterers: 14600 At special positions: 0 Unit cell: (111.552, 131.472, 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: 7.66 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 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " 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 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " 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 63.5% alpha, 5.2% beta 135 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.624A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.634A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (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: 3.864A 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: 3.996A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.664A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.642A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 83 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.624A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.709A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.766A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.835A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.512A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.744A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.536A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 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: 3.581A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.730A 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 36 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.933A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.567A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.509A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.581A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 147 removed outlier: 4.138A pdb=" N ILE L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN L 143 " --> pdb=" O ARG L 139 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.926A 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 removed outlier: 3.521A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.910A 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: 6.378A 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: 7.165A 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 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.578A 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 12 through 16 removed outlier: 9.416A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 8.12 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: 3478 1.34 - 1.46: 4329 1.46 - 1.58: 7030 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.96e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CG LEU E 126 " pdb=" CD1 LEU E 126 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CG LEU B 58 " pdb=" CD1 LEU B 58 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.48e-01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.66: 1561 105.66 - 112.73: 8576 112.73 - 119.81: 5167 119.81 - 126.88: 6041 126.88 - 133.96: 826 Bond angle restraints: 22171 Sorted by residual: angle pdb=" CA ARG L 136 " pdb=" CB ARG L 136 " pdb=" CG ARG L 136 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" CA LEU K 49 " pdb=" CB LEU K 49 " pdb=" CG LEU K 49 " ideal model delta sigma weight residual 116.30 125.53 -9.23 3.50e+00 8.16e-02 6.96e+00 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 126.38 -4.84 1.91e+00 2.74e-01 6.43e+00 angle pdb=" CB LYS C 118 " pdb=" CG LYS C 118 " pdb=" CD LYS C 118 " ideal model delta sigma weight residual 111.30 116.81 -5.51 2.30e+00 1.89e-01 5.73e+00 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 7268 35.62 - 71.24: 1312 71.24 - 106.86: 23 106.86 - 142.48: 0 142.48 - 178.10: 2 Dihedral angle restraints: 8605 sinusoidal: 5467 harmonic: 3138 Sorted by residual: dihedral pdb=" CA ASP L 29 " pdb=" C ASP L 29 " pdb=" N MET L 30 " pdb=" CA MET L 30 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 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 38.10 -178.10 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 74.08 145.92 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2231 0.052 - 0.105: 247 0.105 - 0.157: 36 0.157 - 0.209: 1 0.209 - 0.262: 1 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CB ILE L 137 " pdb=" CA ILE L 137 " pdb=" CG1 ILE L 137 " pdb=" CG2 ILE L 137 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ARG L 136 " pdb=" N ARG L 136 " pdb=" C ARG L 136 " pdb=" CB ARG L 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2513 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 33 " 0.017 2.00e-02 2.50e+03 1.41e-02 4.96e+00 pdb=" CG TRP L 33 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 33 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP L 33 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 33 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 33 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 33 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO K 38 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 43 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.025 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1953 2.76 - 3.47: 19799 3.47 - 4.19: 38184 4.19 - 4.90: 59543 Nonbonded interactions: 119481 Sorted by model distance: nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.331 3.350 nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.331 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.136 2.496 nonbonded pdb=" O ASP L 87 " pdb=" OG SER L 91 " model vdw 2.213 2.440 nonbonded pdb=" ND2 ASN A 108 " pdb=" O GLY B 42 " model vdw 2.222 2.520 ... (remaining 119476 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: 1.330 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: 4.310 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 48.800 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15472 Z= 0.176 Angle : 0.552 9.232 22171 Z= 0.321 Chirality : 0.034 0.262 2516 Planarity : 0.004 0.049 1794 Dihedral : 25.751 178.102 6577 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.26), residues: 1057 helix: 2.28 (0.21), residues: 643 sheet: 1.82 (0.76), residues: 48 loop : -0.85 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 33 HIS 0.007 0.001 HIS L 55 PHE 0.009 0.001 PHE D 65 TYR 0.022 0.001 TYR H 40 ARG 0.008 0.000 ARG L 136 *********************** 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 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8469 (m110) cc_final: 0.8112 (m110) REVERT: C 11 SER cc_start: 0.8505 (t) cc_final: 0.8201 (p) REVERT: D 40 TYR cc_start: 0.9159 (m-80) cc_final: 0.8378 (m-80) REVERT: D 51 ASP cc_start: 0.7966 (p0) cc_final: 0.7740 (p0) REVERT: F 74 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7890 (tm-30) REVERT: L 7 ASN cc_start: 0.9106 (m-40) cc_final: 0.8813 (m110) REVERT: M 1 MET cc_start: 0.8023 (tmm) cc_final: 0.7345 (tmm) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3394 time to fit residues: 99.1462 Evaluate side-chains 164 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15472 Z= 0.221 Angle : 0.570 9.503 22171 Z= 0.328 Chirality : 0.036 0.175 2516 Planarity : 0.004 0.050 1794 Dihedral : 28.769 177.700 4413 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.38 % Allowed : 9.96 % Favored : 87.66 % 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: 1.98 (0.26), residues: 1057 helix: 2.36 (0.21), residues: 650 sheet: 1.88 (0.75), residues: 53 loop : -0.84 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP L 33 HIS 0.008 0.001 HIS K 83 PHE 0.013 0.002 PHE L 50 TYR 0.021 0.002 TYR H 40 ARG 0.005 0.000 ARG D 86 *********************** 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 195 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8457 (m110) cc_final: 0.8218 (m110) REVERT: C 74 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8298 (mttm) REVERT: D 40 TYR cc_start: 0.9168 (m-80) cc_final: 0.8413 (m-80) REVERT: D 51 ASP cc_start: 0.7967 (p0) cc_final: 0.7734 (p0) REVERT: F 73 THR cc_start: 0.9287 (t) cc_final: 0.9019 (m) REVERT: F 74 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7758 (tm-30) REVERT: M 1 MET cc_start: 0.7675 (tmm) cc_final: 0.6966 (tmm) outliers start: 22 outliers final: 17 residues processed: 184 average time/residue: 0.2879 time to fit residues: 76.3829 Evaluate side-chains 180 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15472 Z= 0.328 Angle : 0.607 9.378 22171 Z= 0.349 Chirality : 0.038 0.191 2516 Planarity : 0.005 0.050 1794 Dihedral : 29.027 177.447 4413 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.46 % Allowed : 12.23 % 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: 1.78 (0.26), residues: 1057 helix: 2.22 (0.20), residues: 650 sheet: 1.80 (0.75), residues: 53 loop : -0.95 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 33 HIS 0.004 0.001 HIS K 83 PHE 0.016 0.002 PHE L 50 TYR 0.032 0.002 TYR H 40 ARG 0.005 0.001 ARG D 86 *********************** 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 203 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8491 (m110) cc_final: 0.8254 (m110) REVERT: D 40 TYR cc_start: 0.9200 (m-80) cc_final: 0.8488 (m-80) REVERT: D 51 ASP cc_start: 0.7951 (p0) cc_final: 0.7681 (p0) REVERT: F 73 THR cc_start: 0.9373 (t) cc_final: 0.9120 (m) REVERT: F 74 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7681 (tm-30) REVERT: H 68 ASP cc_start: 0.9117 (t70) cc_final: 0.8746 (t0) REVERT: L 63 LYS cc_start: 0.8956 (mttp) cc_final: 0.8618 (mttp) REVERT: L 79 ASN cc_start: 0.7383 (m-40) cc_final: 0.7183 (m110) REVERT: M 1 MET cc_start: 0.7476 (tmm) cc_final: 0.6607 (tmm) outliers start: 32 outliers final: 21 residues processed: 187 average time/residue: 0.3051 time to fit residues: 80.5139 Evaluate side-chains 183 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1663 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= 0.282 Angle : 0.588 9.524 22171 Z= 0.337 Chirality : 0.037 0.180 2516 Planarity : 0.005 0.049 1794 Dihedral : 29.028 178.160 4413 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.79 % Allowed : 15.15 % Favored : 81.06 % 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: 1.75 (0.26), residues: 1057 helix: 2.28 (0.20), residues: 648 sheet: 1.68 (0.77), residues: 48 loop : -1.07 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 141 HIS 0.006 0.001 HIS L 55 PHE 0.018 0.002 PHE L 50 TYR 0.031 0.002 TYR H 40 ARG 0.005 0.000 ARG D 86 *********************** 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 204 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8735 (pm20) cc_final: 0.8512 (pm20) REVERT: B 25 ASN cc_start: 0.8507 (m110) cc_final: 0.8241 (m110) REVERT: D 40 TYR cc_start: 0.9159 (m-80) cc_final: 0.8439 (m-80) REVERT: D 51 ASP cc_start: 0.8046 (p0) cc_final: 0.7773 (p0) REVERT: E 59 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: F 73 THR cc_start: 0.9378 (t) cc_final: 0.9129 (m) REVERT: F 74 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7619 (tm-30) REVERT: H 68 ASP cc_start: 0.9095 (t70) cc_final: 0.8733 (t0) REVERT: K 83 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.6760 (t-90) REVERT: M 1 MET cc_start: 0.7466 (tmm) cc_final: 0.6746 (tmm) outliers start: 35 outliers final: 25 residues processed: 187 average time/residue: 0.3069 time to fit residues: 80.4913 Evaluate side-chains 191 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15472 Z= 0.305 Angle : 0.601 9.768 22171 Z= 0.343 Chirality : 0.037 0.184 2516 Planarity : 0.005 0.049 1794 Dihedral : 29.096 177.847 4413 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.46 % Allowed : 16.45 % 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: 1.67 (0.26), residues: 1057 helix: 2.20 (0.20), residues: 649 sheet: 1.44 (0.72), residues: 53 loop : -1.08 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP L 33 HIS 0.004 0.001 HIS K 83 PHE 0.018 0.002 PHE L 50 TYR 0.032 0.002 TYR H 40 ARG 0.006 0.000 ARG D 86 *********************** 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 203 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8729 (pm20) cc_final: 0.8506 (pm20) REVERT: B 25 ASN cc_start: 0.8547 (m110) cc_final: 0.8278 (m110) REVERT: C 74 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8467 (mttm) REVERT: D 40 TYR cc_start: 0.9180 (m-80) cc_final: 0.8449 (m-80) REVERT: D 51 ASP cc_start: 0.8079 (p0) cc_final: 0.7804 (p0) REVERT: F 73 THR cc_start: 0.9383 (t) cc_final: 0.9136 (m) REVERT: F 74 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7609 (tm-30) REVERT: H 68 ASP cc_start: 0.9112 (t70) cc_final: 0.8773 (t0) REVERT: L 79 ASN cc_start: 0.6684 (m110) cc_final: 0.6417 (m110) REVERT: M 1 MET cc_start: 0.7531 (tmm) cc_final: 0.7026 (tmm) outliers start: 32 outliers final: 25 residues processed: 187 average time/residue: 0.3147 time to fit residues: 82.0963 Evaluate side-chains 192 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU 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: 7.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15472 Z= 0.223 Angle : 0.574 9.279 22171 Z= 0.329 Chirality : 0.035 0.177 2516 Planarity : 0.004 0.047 1794 Dihedral : 29.031 178.462 4413 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.14 % Allowed : 17.97 % Favored : 78.90 % 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 (0.26), residues: 1057 helix: 2.35 (0.20), residues: 650 sheet: 1.20 (0.70), residues: 53 loop : -1.07 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP L 33 HIS 0.004 0.001 HIS K 65 PHE 0.019 0.001 PHE L 50 TYR 0.032 0.002 TYR H 83 ARG 0.007 0.000 ARG G 99 *********************** 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 203 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8459 (tpp80) cc_final: 0.7979 (ttm110) REVERT: A 59 GLU cc_start: 0.8790 (pm20) cc_final: 0.8570 (pm20) REVERT: B 25 ASN cc_start: 0.8529 (m110) cc_final: 0.8217 (m110) REVERT: C 74 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8469 (mttm) REVERT: D 40 TYR cc_start: 0.9184 (m-80) cc_final: 0.8432 (m-80) REVERT: D 51 ASP cc_start: 0.8056 (p0) cc_final: 0.7799 (p0) REVERT: E 59 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: E 108 ASN cc_start: 0.9446 (t0) cc_final: 0.9009 (t0) REVERT: F 73 THR cc_start: 0.9386 (t) cc_final: 0.9139 (m) REVERT: F 74 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7594 (tm-30) REVERT: H 68 ASP cc_start: 0.9101 (t70) cc_final: 0.8743 (t0) REVERT: L 79 ASN cc_start: 0.6691 (m110) cc_final: 0.6366 (m110) REVERT: M 1 MET cc_start: 0.7489 (tmm) cc_final: 0.7008 (tmm) outliers start: 29 outliers final: 24 residues processed: 189 average time/residue: 0.3071 time to fit residues: 81.1941 Evaluate side-chains 194 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS L 55 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15472 Z= 0.206 Angle : 0.569 8.809 22171 Z= 0.324 Chirality : 0.035 0.177 2516 Planarity : 0.004 0.045 1794 Dihedral : 28.989 178.387 4413 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.57 % Allowed : 18.29 % Favored : 78.14 % 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: 1.85 (0.26), residues: 1057 helix: 2.41 (0.21), residues: 649 sheet: 1.15 (0.71), residues: 53 loop : -1.10 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 33 HIS 0.006 0.001 HIS L 55 PHE 0.020 0.001 PHE L 50 TYR 0.035 0.002 TYR H 83 ARG 0.007 0.000 ARG D 86 *********************** 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: 33 poor density : 171 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8786 (pm20) cc_final: 0.8568 (pm20) REVERT: B 25 ASN cc_start: 0.8539 (m110) cc_final: 0.8229 (m110) REVERT: C 74 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8479 (mttm) REVERT: D 40 TYR cc_start: 0.9218 (m-80) cc_final: 0.8452 (m-80) REVERT: D 51 ASP cc_start: 0.8108 (p0) cc_final: 0.7845 (p0) REVERT: E 59 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: F 73 THR cc_start: 0.9379 (t) cc_final: 0.9126 (m) REVERT: F 74 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7579 (tm-30) REVERT: H 68 ASP cc_start: 0.9091 (t70) cc_final: 0.8731 (t0) REVERT: L 4 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7875 (pttm) REVERT: L 7 ASN cc_start: 0.9097 (m110) cc_final: 0.8755 (m110) REVERT: L 79 ASN cc_start: 0.6660 (m110) cc_final: 0.6335 (m110) REVERT: M 1 MET cc_start: 0.7447 (tmm) cc_final: 0.6986 (tmm) outliers start: 33 outliers final: 25 residues processed: 187 average time/residue: 0.3062 time to fit residues: 80.8306 Evaluate side-chains 192 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 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: 0.0980 chunk 119 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** M 2 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: 0.1980 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= 0.239 Angle : 0.586 9.641 22171 Z= 0.332 Chirality : 0.036 0.181 2516 Planarity : 0.004 0.047 1794 Dihedral : 29.015 178.106 4413 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.57 % Allowed : 18.94 % 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: 1.76 (0.26), residues: 1057 helix: 2.34 (0.20), residues: 649 sheet: 1.27 (0.72), residues: 53 loop : -1.16 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP L 33 HIS 0.006 0.001 HIS K 83 PHE 0.022 0.002 PHE M 45 TYR 0.055 0.002 TYR H 83 ARG 0.008 0.000 ARG G 99 *********************** 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 203 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.8557 (pm20) REVERT: B 25 ASN cc_start: 0.8537 (m110) cc_final: 0.8295 (m110) REVERT: C 74 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8514 (mttm) REVERT: D 40 TYR cc_start: 0.9250 (m-80) cc_final: 0.8542 (m-80) REVERT: D 51 ASP cc_start: 0.8057 (p0) cc_final: 0.7789 (p0) REVERT: E 59 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: F 73 THR cc_start: 0.9394 (t) cc_final: 0.9147 (m) REVERT: F 74 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7561 (tm-30) REVERT: H 68 ASP cc_start: 0.9111 (t70) cc_final: 0.8727 (t0) REVERT: L 7 ASN cc_start: 0.9108 (m110) cc_final: 0.8795 (m110) REVERT: L 79 ASN cc_start: 0.6635 (m110) cc_final: 0.6320 (m110) REVERT: M 1 MET cc_start: 0.7522 (tmm) cc_final: 0.7125 (tmm) outliers start: 33 outliers final: 27 residues processed: 188 average time/residue: 0.3055 time to fit residues: 81.3226 Evaluate side-chains 196 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1988 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= 0.212 Angle : 0.575 10.391 22171 Z= 0.327 Chirality : 0.035 0.180 2516 Planarity : 0.004 0.046 1794 Dihedral : 28.995 178.368 4413 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.46 % Allowed : 19.05 % 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: 1.80 (0.26), residues: 1057 helix: 2.37 (0.21), residues: 649 sheet: 1.26 (0.72), residues: 53 loop : -1.14 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.005 TRP L 141 HIS 0.007 0.001 HIS K 83 PHE 0.020 0.001 PHE L 50 TYR 0.055 0.002 TYR H 83 ARG 0.008 0.000 ARG G 99 *********************** 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 202 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8815 (pm20) cc_final: 0.8606 (pm20) REVERT: B 25 ASN cc_start: 0.8507 (m110) cc_final: 0.8126 (m110) REVERT: C 74 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8515 (mttm) REVERT: D 40 TYR cc_start: 0.9242 (m-80) cc_final: 0.8549 (m-80) REVERT: D 51 ASP cc_start: 0.8117 (p0) cc_final: 0.7853 (p0) REVERT: E 59 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: F 74 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7642 (tm-30) REVERT: H 68 ASP cc_start: 0.9078 (t70) cc_final: 0.8734 (t0) REVERT: L 7 ASN cc_start: 0.9094 (m110) cc_final: 0.8773 (m110) REVERT: L 79 ASN cc_start: 0.6596 (m110) cc_final: 0.6279 (m110) REVERT: M 1 MET cc_start: 0.7533 (tmm) cc_final: 0.7146 (tmm) outliers start: 32 outliers final: 29 residues processed: 188 average time/residue: 0.2998 time to fit residues: 79.6036 Evaluate side-chains 199 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain M residue 3 ILE 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: 1.9990 chunk 85 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2054 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= 0.244 Angle : 0.590 10.753 22171 Z= 0.334 Chirality : 0.036 0.181 2516 Planarity : 0.004 0.046 1794 Dihedral : 29.015 178.108 4413 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.25 % Allowed : 19.91 % Favored : 76.84 % 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: 1.72 (0.26), residues: 1057 helix: 2.31 (0.21), residues: 649 sheet: 1.18 (0.73), residues: 53 loop : -1.18 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP L 141 HIS 0.013 0.001 HIS K 83 PHE 0.021 0.002 PHE L 50 TYR 0.056 0.002 TYR H 83 ARG 0.007 0.000 ARG G 99 ********************** 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 202 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8812 (pm20) cc_final: 0.8574 (pm20) REVERT: B 25 ASN cc_start: 0.8527 (m110) cc_final: 0.8203 (m110) REVERT: C 74 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8516 (mttm) REVERT: D 40 TYR cc_start: 0.9257 (m-80) cc_final: 0.8552 (m-80) REVERT: D 51 ASP cc_start: 0.8058 (p0) cc_final: 0.7799 (p0) REVERT: E 59 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: F 74 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7641 (tm-30) REVERT: H 68 ASP cc_start: 0.9111 (t70) cc_final: 0.8758 (t0) REVERT: L 7 ASN cc_start: 0.9088 (m110) cc_final: 0.8758 (m110) REVERT: L 79 ASN cc_start: 0.6596 (m110) cc_final: 0.6285 (m110) REVERT: M 1 MET cc_start: 0.7530 (tmm) cc_final: 0.7153 (tmm) outliers start: 30 outliers final: 28 residues processed: 188 average time/residue: 0.3153 time to fit residues: 83.1736 Evaluate side-chains 199 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.091808 restraints weight = 37051.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.091173 restraints weight = 22825.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.092131 restraints weight = 19421.917| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2067 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= 0.213 Angle : 0.581 10.350 22171 Z= 0.328 Chirality : 0.035 0.186 2516 Planarity : 0.004 0.046 1794 Dihedral : 28.983 178.430 4413 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.92 % Allowed : 20.35 % Favored : 76.73 % 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: 1.75 (0.26), residues: 1057 helix: 2.35 (0.21), residues: 649 sheet: 1.16 (0.73), residues: 53 loop : -1.17 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP L 141 HIS 0.005 0.001 HIS L 55 PHE 0.021 0.001 PHE L 50 TYR 0.048 0.002 TYR H 83 ARG 0.007 0.000 ARG G 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.05 seconds wall clock time: 47 minutes 18.94 seconds (2838.94 seconds total)