Starting phenix.real_space_refine on Sun Nov 17 17:44:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn5_40613/11_2024/8sn5_40613.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn5_40613/11_2024/8sn5_40613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn5_40613/11_2024/8sn5_40613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn5_40613/11_2024/8sn5_40613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn5_40613/11_2024/8sn5_40613.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn5_40613/11_2024/8sn5_40613.cif" } resolution = 3.9 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= 0.003 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. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14600 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 32.772 74.839 47.610 1.00 92.05 S ATOM 12446 SG CYS K 51 33.544 71.534 45.841 1.00 78.30 S ATOM 12470 SG CYS K 54 32.537 74.397 43.794 1.00100.28 S ATOM 12187 SG CYS K 16 22.380 68.849 53.466 1.00109.61 S ATOM 12205 SG CYS K 19 20.326 66.237 55.227 1.00105.23 S ATOM 12335 SG CYS K 36 23.285 67.916 57.089 1.00 94.72 S ATOM 12357 SG CYS K 39 24.037 65.484 54.484 1.00 92.21 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: 9.17, per 1000 atoms: 0.63 Number of scatterers: 14600 At special positions: 0 Unit cell: (108.896, 134.128, 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 - 3.00 Amino acid : True - 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: 3.02 Conformation dependent library (CDL) restraints added in 1.3 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 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " 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: 48 helices and 13 sheets defined 63.6% alpha, 5.3% beta 135 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.502A 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: 3.794A 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: 3.921A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.203A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.476A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.813A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.725A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.708A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.803A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 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: 3.571A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.543A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.571A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 15 removed outlier: 3.619A 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: 3.596A 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: 3.702A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.773A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 4.256A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.679A 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: 3.738A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.809A 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: 6.826A 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: 7.004A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.679A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28 removed outlier: 4.096A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16 removed outlier: 3.623A pdb=" N VAL M 5 " --> pdb=" O ILE M 13 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 15 " --> pdb=" O ILE M 3 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE M 3 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG M 42 " --> pdb=" O VAL M 70 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 3.61 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: 3384 1.34 - 1.45: 4369 1.45 - 1.57: 7084 1.57 - 1.69: 586 1.69 - 1.81: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CA ILE B 29 " pdb=" CB ILE B 29 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.26e+00 bond pdb=" CB LYS M 48 " pdb=" CG LYS M 48 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" C VAL K 24 " pdb=" N GLU K 25 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.15e+00 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.29e-01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 21557 1.54 - 3.07: 551 3.07 - 4.61: 41 4.61 - 6.14: 16 6.14 - 7.68: 6 Bond angle restraints: 22171 Sorted by residual: angle pdb=" N TRP L 141 " pdb=" CA TRP L 141 " pdb=" CB TRP L 141 " ideal model delta sigma weight residual 110.12 115.65 -5.53 1.47e+00 4.63e-01 1.41e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.89 -6.35 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CB LYS M 48 " pdb=" CG LYS M 48 " pdb=" CD LYS M 48 " ideal model delta sigma weight residual 111.30 118.73 -7.43 2.30e+00 1.89e-01 1.04e+01 angle pdb=" C GLU L 140 " pdb=" N TRP L 141 " pdb=" CA TRP L 141 " ideal model delta sigma weight residual 120.28 115.98 4.30 1.34e+00 5.57e-01 1.03e+01 angle pdb=" CA TRP L 141 " pdb=" CB TRP L 141 " pdb=" CG TRP L 141 " ideal model delta sigma weight residual 113.60 118.60 -5.00 1.90e+00 2.77e-01 6.93e+00 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 7295 35.68 - 71.35: 1292 71.35 - 107.03: 16 107.03 - 142.70: 0 142.70 - 178.38: 2 Dihedral angle restraints: 8605 sinusoidal: 5467 harmonic: 3138 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.38 -178.38 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 76.32 143.68 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA ARG L 131 " pdb=" C ARG L 131 " pdb=" N ASP L 132 " pdb=" CA ASP L 132 " ideal model delta harmonic sigma weight residual -180.00 -162.15 -17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1794 0.031 - 0.061: 526 0.061 - 0.092: 118 0.092 - 0.123: 66 0.123 - 0.153: 12 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA GLU K 25 " pdb=" N GLU K 25 " pdb=" C GLU K 25 " pdb=" CB GLU K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 2513 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 141 " 0.030 2.00e-02 2.50e+03 2.98e-02 2.23e+01 pdb=" CG TRP L 141 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP L 141 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP L 141 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 141 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 141 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 141 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 141 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 141 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.022 2.00e-02 2.50e+03 9.23e-03 2.34e+00 pdb=" N9 DA I -35 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.008 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 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -54 " 0.020 2.00e-02 2.50e+03 9.03e-03 2.24e+00 pdb=" N9 DA I -54 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA I -54 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I -54 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I -54 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -54 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I -54 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I -54 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA I -54 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -54 " -0.002 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1914 2.76 - 3.47: 20004 3.47 - 4.19: 38245 4.19 - 4.90: 59218 Nonbonded interactions: 119383 Sorted by model distance: nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.329 3.350 nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.330 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.131 2.496 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.178 3.040 nonbonded pdb=" OG SER L 91 " pdb=" OE1 GLN L 92 " model vdw 2.221 3.040 ... (remaining 119378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.920 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.160 Process input model: 40.570 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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= 0.185 Angle : 0.569 7.680 22171 Z= 0.329 Chirality : 0.035 0.153 2516 Planarity : 0.004 0.037 1794 Dihedral : 25.638 178.379 6577 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.27), residues: 1057 helix: 2.63 (0.21), residues: 646 sheet: 0.85 (0.75), residues: 47 loop : -0.56 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.005 TRP L 141 HIS 0.005 0.001 HIS D 109 PHE 0.006 0.001 PHE D 70 TYR 0.018 0.001 TYR H 40 ARG 0.006 0.000 ARG L 131 *********************** 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 284 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.248 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9152 (mt) cc_final: 0.8940 (mt) REVERT: C 39 TYR cc_start: 0.8837 (m-80) cc_final: 0.8516 (m-80) REVERT: D 108 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8001 (mtmt) REVERT: H 35 GLU cc_start: 0.8641 (mp0) cc_final: 0.8421 (mp0) REVERT: H 89 ILE cc_start: 0.9224 (mt) cc_final: 0.9005 (mt) REVERT: K 13 GLU cc_start: 0.8434 (tp30) cc_final: 0.8139 (tm-30) REVERT: L 60 TYR cc_start: 0.7143 (t80) cc_final: 0.6810 (t80) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3455 time to fit residues: 132.9004 Evaluate side-chains 226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.0070 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 38 ASN K 81 GLN K 83 HIS L 46 GLN M 2 GLN M 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1283 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= 0.203 Angle : 0.587 11.118 22171 Z= 0.336 Chirality : 0.036 0.161 2516 Planarity : 0.004 0.043 1794 Dihedral : 28.848 178.608 4413 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.30 % Allowed : 13.10 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.27), residues: 1057 helix: 2.60 (0.21), residues: 653 sheet: 0.57 (0.70), residues: 50 loop : -0.61 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP L 141 HIS 0.006 0.001 HIS L 75 PHE 0.014 0.001 PHE L 62 TYR 0.015 0.002 TYR L 74 ARG 0.007 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 256 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 245 time to evaluate : 1.217 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9072 (t) cc_final: 0.7785 (t) REVERT: A 59 GLU cc_start: 0.8851 (pm20) cc_final: 0.8427 (pm20) REVERT: A 120 MET cc_start: 0.8006 (mtt) cc_final: 0.7696 (mtt) REVERT: A 125 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: C 110 ASN cc_start: 0.8573 (p0) cc_final: 0.8357 (p0) REVERT: D 88 THR cc_start: 0.9297 (m) cc_final: 0.8869 (p) REVERT: D 108 LYS cc_start: 0.8272 (ttpt) cc_final: 0.8039 (mtmt) REVERT: L 60 TYR cc_start: 0.7206 (t80) cc_final: 0.6851 (t80) REVERT: L 88 ILE cc_start: 0.8460 (mp) cc_final: 0.8259 (mp) outliers start: 11 outliers final: 8 residues processed: 250 average time/residue: 0.3103 time to fit residues: 107.9971 Evaluate side-chains 228 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 TYR Chi-restraints excluded: chain M residue 68 HIS 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: 4.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 38 ASN H 47 GLN K 32 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 HIS M 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1646 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= 0.242 Angle : 0.588 11.891 22171 Z= 0.335 Chirality : 0.036 0.144 2516 Planarity : 0.004 0.045 1794 Dihedral : 28.986 178.692 4413 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.16 % Allowed : 13.96 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.26), residues: 1057 helix: 2.49 (0.21), residues: 652 sheet: 0.72 (0.67), residues: 49 loop : -0.70 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 141 HIS 0.004 0.001 HIS D 109 PHE 0.014 0.001 PHE L 62 TYR 0.015 0.002 TYR F 88 ARG 0.005 0.000 ARG G 71 *********************** 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 248 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 1.095 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: symmetry clash REVERT: A 57 SER cc_start: 0.9026 (t) cc_final: 0.7554 (t) REVERT: A 59 GLU cc_start: 0.8793 (pm20) cc_final: 0.8147 (pm20) REVERT: A 120 MET cc_start: 0.8179 (mtt) cc_final: 0.7848 (mtt) REVERT: A 125 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: C 110 ASN cc_start: 0.8676 (p0) cc_final: 0.8435 (p0) REVERT: D 108 LYS cc_start: 0.8297 (ttpt) cc_final: 0.8037 (mtpt) REVERT: E 59 GLU cc_start: 0.7730 (pm20) cc_final: 0.7504 (pm20) REVERT: F 88 TYR cc_start: 0.8661 (m-80) cc_final: 0.8042 (m-80) REVERT: G 118 LYS cc_start: 0.8093 (tmtt) cc_final: 0.7814 (tmtt) REVERT: H 79 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.8041 (ttm-80) REVERT: K 68 ARG cc_start: 0.6898 (mtm110) cc_final: 0.6115 (mtm110) REVERT: L 60 TYR cc_start: 0.7463 (t80) cc_final: 0.7116 (t80) REVERT: L 88 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8114 (mp) REVERT: L 134 TYR cc_start: 0.6849 (t80) cc_final: 0.6512 (t80) outliers start: 19 outliers final: 12 residues processed: 235 average time/residue: 0.3599 time to fit residues: 119.1381 Evaluate side-chains 226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS 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: 1.9990 chunk 12 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 38 ASN K 41 GLN L 46 GLN ** L 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 GLN M 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15472 Z= 0.268 Angle : 0.600 11.490 22171 Z= 0.341 Chirality : 0.036 0.166 2516 Planarity : 0.004 0.043 1794 Dihedral : 29.100 179.099 4413 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.71 % Allowed : 16.77 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.27), residues: 1057 helix: 2.32 (0.21), residues: 660 sheet: 0.81 (0.67), residues: 48 loop : -0.85 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 141 HIS 0.008 0.001 HIS K 65 PHE 0.014 0.001 PHE L 62 TYR 0.020 0.002 TYR L 74 ARG 0.007 0.000 ARG G 71 *********************** 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 251 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.161 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: A 57 SER cc_start: 0.9031 (t) cc_final: 0.7681 (t) REVERT: A 59 GLU cc_start: 0.8943 (pm20) cc_final: 0.8046 (pm20) REVERT: A 125 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: B 88 TYR cc_start: 0.8024 (m-80) cc_final: 0.7558 (m-80) REVERT: D 33 ARG cc_start: 0.7649 (mtp-110) cc_final: 0.7178 (mtm110) REVERT: D 108 LYS cc_start: 0.8338 (ttpt) cc_final: 0.8039 (mtpt) REVERT: F 88 TYR cc_start: 0.8897 (m-80) cc_final: 0.7317 (m-10) REVERT: H 51 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8226 (t0) REVERT: H 83 TYR cc_start: 0.7442 (m-10) cc_final: 0.7142 (m-10) REVERT: K 37 LYS cc_start: 0.9195 (tptt) cc_final: 0.8714 (tptt) REVERT: K 41 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8582 (tp40) REVERT: L 31 PHE cc_start: 0.7840 (m-10) cc_final: 0.7566 (m-80) REVERT: L 60 TYR cc_start: 0.7500 (t80) cc_final: 0.7198 (t80) REVERT: L 88 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8156 (mp) outliers start: 24 outliers final: 17 residues processed: 234 average time/residue: 0.3222 time to fit residues: 104.7949 Evaluate side-chains 233 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS 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: 0.7980 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 0.0170 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 41 GLN L 55 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15472 Z= 0.245 Angle : 0.599 12.139 22171 Z= 0.340 Chirality : 0.036 0.162 2516 Planarity : 0.004 0.047 1794 Dihedral : 29.089 179.449 4413 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.49 % Allowed : 18.40 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.26), residues: 1057 helix: 2.35 (0.20), residues: 659 sheet: 0.62 (0.66), residues: 48 loop : -0.88 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 141 HIS 0.010 0.001 HIS K 65 PHE 0.016 0.001 PHE L 62 TYR 0.017 0.002 TYR E 99 ARG 0.006 0.000 ARG G 71 *********************** 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 245 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 1.123 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: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9011 (t) cc_final: 0.7580 (t) REVERT: A 59 GLU cc_start: 0.8959 (pm20) cc_final: 0.8052 (pm20) REVERT: A 125 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: D 33 ARG cc_start: 0.7691 (mtp-110) cc_final: 0.7202 (mtm110) REVERT: D 108 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8067 (mtpt) REVERT: E 39 HIS cc_start: 0.8166 (t-90) cc_final: 0.7964 (t-90) REVERT: F 88 TYR cc_start: 0.8973 (m-80) cc_final: 0.8670 (m-10) REVERT: G 24 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8381 (mm-40) REVERT: H 35 GLU cc_start: 0.8632 (mp0) cc_final: 0.8404 (mp0) REVERT: H 40 TYR cc_start: 0.9199 (m-80) cc_final: 0.8812 (m-80) REVERT: H 51 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8221 (t0) REVERT: K 37 LYS cc_start: 0.9246 (tptt) cc_final: 0.8660 (tptt) REVERT: K 41 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8450 (tp40) REVERT: K 68 ARG cc_start: 0.6883 (mtm110) cc_final: 0.6032 (mtm110) REVERT: L 60 TYR cc_start: 0.7383 (t80) cc_final: 0.7086 (t80) REVERT: L 88 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8210 (mp) outliers start: 22 outliers final: 16 residues processed: 232 average time/residue: 0.3052 time to fit residues: 99.6347 Evaluate side-chains 232 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 41 GLN L 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2297 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= 0.227 Angle : 0.602 12.724 22171 Z= 0.338 Chirality : 0.036 0.157 2516 Planarity : 0.004 0.050 1794 Dihedral : 29.061 179.519 4413 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.71 % Allowed : 19.05 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.27), residues: 1057 helix: 2.38 (0.21), residues: 660 sheet: 0.36 (0.68), residues: 48 loop : -0.87 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP L 141 HIS 0.009 0.001 HIS K 65 PHE 0.014 0.001 PHE L 62 TYR 0.018 0.002 TYR E 99 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 1.085 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: symmetry clash REVERT: A 57 SER cc_start: 0.9005 (t) cc_final: 0.7580 (t) REVERT: A 59 GLU cc_start: 0.8897 (pm20) cc_final: 0.7917 (pm20) REVERT: A 125 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: D 108 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8054 (mtpt) REVERT: F 88 TYR cc_start: 0.9008 (m-80) cc_final: 0.8739 (m-10) REVERT: H 35 GLU cc_start: 0.8629 (mp0) cc_final: 0.8405 (mp0) REVERT: H 40 TYR cc_start: 0.9207 (m-80) cc_final: 0.8848 (m-80) REVERT: H 51 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8209 (t0) REVERT: K 21 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7252 (mm-30) REVERT: K 37 LYS cc_start: 0.9211 (tptt) cc_final: 0.8679 (tptt) REVERT: K 41 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8527 (tp40) REVERT: K 68 ARG cc_start: 0.6887 (mtm110) cc_final: 0.6407 (mtm110) REVERT: K 84 TYR cc_start: 0.7644 (m-80) cc_final: 0.6726 (m-80) REVERT: M 1 MET cc_start: 0.5444 (tmm) cc_final: 0.4807 (tpt) outliers start: 24 outliers final: 18 residues processed: 234 average time/residue: 0.2978 time to fit residues: 98.2925 Evaluate side-chains 240 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 41 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15472 Z= 0.195 Angle : 0.598 12.917 22171 Z= 0.336 Chirality : 0.035 0.157 2516 Planarity : 0.004 0.054 1794 Dihedral : 29.012 179.502 4413 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.49 % Allowed : 19.81 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.27), residues: 1057 helix: 2.43 (0.21), residues: 658 sheet: 0.23 (0.69), residues: 48 loop : -0.88 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 141 HIS 0.009 0.001 HIS K 65 PHE 0.014 0.001 PHE L 62 TYR 0.033 0.002 TYR L 134 ARG 0.006 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 250 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8755 (m-30) cc_final: 0.8467 (m-30) REVERT: A 125 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: D 33 ARG cc_start: 0.7676 (mtm110) cc_final: 0.6918 (mtp-110) REVERT: D 108 LYS cc_start: 0.8301 (ttpt) cc_final: 0.8037 (mtpt) REVERT: E 61 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9203 (mm) REVERT: F 88 TYR cc_start: 0.8970 (m-80) cc_final: 0.8747 (m-10) REVERT: H 35 GLU cc_start: 0.8635 (mp0) cc_final: 0.8408 (mp0) REVERT: H 40 TYR cc_start: 0.9179 (m-80) cc_final: 0.8802 (m-80) REVERT: H 51 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8200 (t0) REVERT: K 37 LYS cc_start: 0.9194 (tptt) cc_final: 0.8487 (tptt) REVERT: K 41 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8263 (tp40) REVERT: K 68 ARG cc_start: 0.6922 (mtm110) cc_final: 0.6492 (mtm110) REVERT: K 84 TYR cc_start: 0.7642 (m-80) cc_final: 0.6694 (m-80) REVERT: M 1 MET cc_start: 0.5036 (tmm) cc_final: 0.4534 (tpt) outliers start: 22 outliers final: 15 residues processed: 237 average time/residue: 0.3028 time to fit residues: 100.2589 Evaluate side-chains 236 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 38 ASN K 41 GLN L 7 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15472 Z= 0.184 Angle : 0.605 13.924 22171 Z= 0.337 Chirality : 0.035 0.159 2516 Planarity : 0.004 0.053 1794 Dihedral : 28.995 179.163 4413 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.49 % Allowed : 20.35 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.27), residues: 1057 helix: 2.49 (0.21), residues: 659 sheet: -0.11 (0.68), residues: 42 loop : -0.89 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.005 TRP L 141 HIS 0.008 0.001 HIS K 65 PHE 0.012 0.001 PHE L 62 TYR 0.042 0.002 TYR L 145 ARG 0.007 0.000 ARG D 86 *********************** 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 243 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 1.205 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: A 59 GLU cc_start: 0.8777 (pm20) cc_final: 0.8397 (pm20) REVERT: A 123 ASP cc_start: 0.8739 (m-30) cc_final: 0.8426 (m-30) REVERT: A 125 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: D 108 LYS cc_start: 0.8296 (ttpt) cc_final: 0.8035 (mtpt) REVERT: E 61 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9174 (mm) REVERT: H 35 GLU cc_start: 0.8623 (mp0) cc_final: 0.8393 (mp0) REVERT: H 40 TYR cc_start: 0.9157 (m-80) cc_final: 0.8784 (m-80) REVERT: H 51 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8176 (t0) REVERT: K 37 LYS cc_start: 0.9186 (tptt) cc_final: 0.8636 (tptt) REVERT: K 41 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8517 (tp40) REVERT: K 68 ARG cc_start: 0.6936 (mtm110) cc_final: 0.6512 (mtm110) REVERT: K 84 TYR cc_start: 0.7606 (m-80) cc_final: 0.6647 (m-80) REVERT: L 110 LEU cc_start: 0.9100 (pp) cc_final: 0.8747 (tt) REVERT: M 1 MET cc_start: 0.4716 (tmm) cc_final: 0.4260 (tpt) outliers start: 22 outliers final: 16 residues processed: 229 average time/residue: 0.3041 time to fit residues: 98.6898 Evaluate side-chains 235 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL 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 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2545 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= 0.206 Angle : 0.620 13.843 22171 Z= 0.346 Chirality : 0.035 0.190 2516 Planarity : 0.004 0.055 1794 Dihedral : 29.024 178.773 4413 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.49 % Allowed : 21.21 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.27), residues: 1057 helix: 2.45 (0.21), residues: 659 sheet: 0.28 (0.69), residues: 47 loop : -0.94 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP L 141 HIS 0.008 0.001 HIS K 65 PHE 0.014 0.001 PHE L 62 TYR 0.022 0.002 TYR F 88 ARG 0.006 0.000 ARG D 86 *********************** 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 243 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 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: symmetry clash REVERT: A 59 GLU cc_start: 0.8760 (pm20) cc_final: 0.8316 (pm20) REVERT: A 123 ASP cc_start: 0.8751 (m-30) cc_final: 0.8470 (m-30) REVERT: A 125 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: D 59 MET cc_start: 0.8504 (tpp) cc_final: 0.7920 (tpp) REVERT: D 108 LYS cc_start: 0.8313 (ttpt) cc_final: 0.8058 (mtpt) REVERT: E 61 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9173 (mm) REVERT: H 35 GLU cc_start: 0.8619 (mp0) cc_final: 0.8400 (mp0) REVERT: H 40 TYR cc_start: 0.9175 (m-80) cc_final: 0.8800 (m-80) REVERT: H 51 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8191 (t0) REVERT: K 37 LYS cc_start: 0.9206 (tptt) cc_final: 0.8518 (tptt) REVERT: K 41 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8314 (tp40) REVERT: K 68 ARG cc_start: 0.6904 (mtm110) cc_final: 0.6631 (mtm110) REVERT: K 84 TYR cc_start: 0.7596 (m-80) cc_final: 0.6641 (m-80) REVERT: M 1 MET cc_start: 0.4724 (tmm) cc_final: 0.4258 (tpt) outliers start: 22 outliers final: 16 residues processed: 229 average time/residue: 0.2975 time to fit residues: 95.8361 Evaluate side-chains 236 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL 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 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 68 HIS 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: 3.9990 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 118 optimal weight: 0.2980 chunk 102 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15472 Z= 0.310 Angle : 0.676 13.519 22171 Z= 0.375 Chirality : 0.038 0.210 2516 Planarity : 0.005 0.058 1794 Dihedral : 29.153 178.355 4413 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.60 % Allowed : 21.54 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.27), residues: 1057 helix: 2.27 (0.21), residues: 659 sheet: 0.18 (0.69), residues: 47 loop : -0.99 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.005 TRP L 141 HIS 0.009 0.001 HIS K 65 PHE 0.013 0.001 PHE L 62 TYR 0.028 0.002 TYR K 64 ARG 0.005 0.000 ARG D 86 ********************** 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 238 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 1.241 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: 0.8828 (pm20) cc_final: 0.8360 (pm20) REVERT: A 125 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: D 108 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8083 (mtpt) REVERT: E 61 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9195 (mm) REVERT: H 35 GLU cc_start: 0.8602 (mp0) cc_final: 0.8368 (mp0) REVERT: H 40 TYR cc_start: 0.9251 (m-80) cc_final: 0.8947 (m-80) REVERT: H 51 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8262 (t0) REVERT: H 79 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: K 84 TYR cc_start: 0.7642 (m-80) cc_final: 0.6655 (m-80) REVERT: M 1 MET cc_start: 0.5008 (tmm) cc_final: 0.4547 (tpt) outliers start: 23 outliers final: 17 residues processed: 226 average time/residue: 0.3149 time to fit residues: 100.5793 Evaluate side-chains 228 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.0050 chunk 42 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 75 HIS ** 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 = 0.3690 r_free = 0.3690 target = 0.120624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.082108 restraints weight = 47825.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081929 restraints weight = 30185.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.082270 restraints weight = 31757.356| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15472 Z= 0.196 Angle : 0.643 13.897 22171 Z= 0.356 Chirality : 0.036 0.178 2516 Planarity : 0.004 0.048 1794 Dihedral : 29.066 179.220 4413 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.16 % Allowed : 22.08 % Favored : 75.76 % 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 (0.27), residues: 1057 helix: 2.36 (0.21), residues: 657 sheet: 0.06 (0.70), residues: 47 loop : -1.01 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP L 141 HIS 0.009 0.001 HIS K 65 PHE 0.014 0.001 PHE A 67 TYR 0.036 0.002 TYR K 64 ARG 0.007 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.21 seconds wall clock time: 51 minutes 50.21 seconds (3110.21 seconds total)