Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 16:14:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Bad HELIX record, was skipped: HELIX 1 AA1 ASPAAA 5 SERAAA 50 1 46 Bad HELIX record, was skipped: HELIX 2 AA2 PROBBB 6 SERBBB 50 1 45 Bad HELIX record, was skipped: HELIX 3 AA3 PROCCC 6 SERCCC 50 1 45 Bad HELIX record, was skipped: HELIX 4 AA4 PRODDD 6 SERDDD 50 1 45 Bad HELIX record, was skipped: HELIX 5 AA5 PROEEE 6 SEREEE 50 1 45 Bad HELIX record, was skipped: HELIX 6 AA6 PROAaA 6 SERAaA 50 1 45 Bad HELIX record, was skipped: HELIX 7 AA7 PROBaB 6 SERBaB 50 1 45 Bad HELIX record, was skipped: HELIX 8 AA8 PROCaC 6 SERCaC 50 1 45 Bad HELIX record, was skipped: HELIX 9 AA9 PRODaD 6 SERDaD 50 1 45 Bad HELIX record, was skipped: HELIX 10 AB1 PROEaE 6 SEREaE 50 1 45 Bad HELIX record, was skipped: HELIX 11 AB2 PROAbA 6 SERAbA 50 1 45 Bad HELIX record, was skipped: HELIX 12 AB3 PROBbB 6 SERBbB 50 1 45 Bad HELIX record, was skipped: HELIX 13 AB4 PROCbC 6 SERCbC 50 1 45 Bad HELIX record, was skipped: HELIX 14 AB5 PRODbD 6 SERDbD 50 1 45 Bad HELIX record, was skipped: HELIX 15 AB6 PROEbE 6 SEREbE 50 1 45 Bad HELIX record, was skipped: HELIX 16 AB7 PROAcA 6 SERAcA 50 1 45 Bad HELIX record, was skipped: HELIX 17 AB8 PROBcB 6 SERBcB 50 1 45 Bad HELIX record, was skipped: HELIX 18 AB9 PROCcC 6 SERCcC 50 1 45 Bad HELIX record, was skipped: HELIX 19 AC1 PRODcD 6 SERDcD 50 1 45 Bad HELIX record, was skipped: HELIX 20 AC2 PROEcE 6 SEREcE 50 1 45 Bad HELIX record, was skipped: HELIX 21 AC3 PROAdA 6 SERAdA 50 1 45 Bad HELIX record, was skipped: HELIX 22 AC4 PROBdB 6 SERBdB 50 1 45 Bad HELIX record, was skipped: HELIX 23 AC5 PROCdC 6 SERCdC 50 1 45 Bad HELIX record, was skipped: HELIX 24 AC6 PRODdD 6 SERDdD 50 1 45 Bad HELIX record, was skipped: HELIX 25 AC7 PROEdE 6 SEREdE 50 1 45 Bad HELIX record, was skipped: HELIX 26 AC8 PROAeA 6 SERAeA 50 1 45 Bad HELIX record, was skipped: HELIX 27 AC9 PROBeB 6 SERBeB 50 1 45 Bad HELIX record, was skipped: HELIX 28 AD1 PROCeC 6 SERCeC 50 1 45 Bad HELIX record, was skipped: HELIX 29 AD2 PRODeD 6 SERDeD 50 1 45 Bad HELIX record, was skipped: HELIX 30 AD3 PROEeE 6 SEREeE 50 1 45 Bad HELIX record, was skipped: HELIX 31 AD4 PROAfA 6 SERAfA 50 1 45 Bad HELIX record, was skipped: HELIX 32 AD5 PROBfB 6 SERBfB 50 1 45 Bad HELIX record, was skipped: HELIX 33 AD6 PROCfC 6 SERCfC 50 1 45 Bad HELIX record, was skipped: HELIX 34 AD7 PRODfD 6 SERDfD 50 1 45 Bad HELIX record, was skipped: HELIX 35 AD8 PROEfE 6 SEREfE 50 1 45 Bad HELIX record, was skipped: HELIX 36 AD9 SERAgA 17 SERAgA 50 1 34 Bad HELIX record, was skipped: HELIX 37 AE1 SERBgB 17 SERBgB 50 1 34 Bad HELIX record, was skipped: HELIX 38 AE2 SERCgC 17 SERCgC 50 1 34 Bad HELIX record, was skipped: HELIX 39 AE3 SERDgD 17 SERDgD 50 1 34 Bad HELIX record, was skipped: HELIX 40 AE4 SEREgE 17 SEREgE 50 1 34 Bad HELIX record, was skipped: HELIX 41 AE5 PROAhA 6 SERAhA 50 1 45 Bad HELIX record, was skipped: HELIX 42 AE6 PROBhB 6 SERBhB 50 1 45 Bad HELIX record, was skipped: HELIX 43 AE7 PROChC 6 SERChC 50 1 45 Bad HELIX record, was skipped: HELIX 44 AE8 PRODhD 6 SERDhD 50 1 45 Bad HELIX record, was skipped: HELIX 45 AE9 PROEhE 6 SEREhE 50 1 45 Bad HELIX record, was skipped: HELIX 46 AF1 PROAiA 6 SERAiA 50 1 45 Bad HELIX record, was skipped: HELIX 47 AF2 PROBiB 6 SERBiB 50 1 45 Bad HELIX record, was skipped: HELIX 48 AF3 PROCiC 6 SERCiC 50 1 45 Bad HELIX record, was skipped: HELIX 49 AF4 PRODiD 6 SERDiD 50 1 45 Bad HELIX record, was skipped: HELIX 50 AF5 PROEiE 6 SEREiE 50 1 45 Bad HELIX record, was skipped: HELIX 51 AF6 PROAjA 6 SERAjA 50 1 45 Bad HELIX record, was skipped: HELIX 52 AF7 PROBjB 6 SERBjB 50 1 45 Bad HELIX record, was skipped: HELIX 53 AF8 PROCjC 6 SERCjC 50 1 45 Bad HELIX record, was skipped: HELIX 54 AF9 PRODjD 6 SERDjD 50 1 45 Bad HELIX record, was skipped: HELIX 55 AG1 PROEjE 6 SEREjE 50 1 45 Bad HELIX record, was skipped: HELIX 56 AG2 PROAkA 6 SERAkA 50 1 45 Bad HELIX record, was skipped: HELIX 57 AG3 PROBkB 6 SERBkB 50 1 45 Bad HELIX record, was skipped: HELIX 58 AG4 PROCkC 6 SERCkC 50 1 45 Bad HELIX record, was skipped: HELIX 59 AG5 PRODkD 6 SERDkD 50 1 45 Bad HELIX record, was skipped: HELIX 60 AG6 PROEkE 6 SEREkE 50 1 45 Bad HELIX record, was skipped: HELIX 61 AG7 PROAlA 6 SERAlA 50 1 45 Bad HELIX record, was skipped: HELIX 62 AG8 PROBlB 6 SERBlB 50 1 45 Bad HELIX record, was skipped: HELIX 63 AG9 PROClC 6 SERClC 50 1 45 Bad HELIX record, was skipped: HELIX 64 AH1 PRODlD 6 SERDlD 50 1 45 Bad HELIX record, was skipped: HELIX 65 AH2 PROElE 6 SERElE 50 1 45 Bad HELIX record, was skipped: HELIX 66 AH3 PROAmA 6 SERAmA 50 1 45 Bad HELIX record, was skipped: HELIX 67 AH4 PROBmB 6 SERBmB 50 1 45 Bad HELIX record, was skipped: HELIX 68 AH5 PROCmC 6 SERCmC 50 1 45 Bad HELIX record, was skipped: HELIX 69 AH6 PRODmD 6 SERDmD 50 1 45 Bad HELIX record, was skipped: HELIX 70 AH7 PROEmE 6 SEREmE 50 1 45 Bad HELIX record, was skipped: HELIX 71 AH8 PROAnA 6 SERAnA 50 1 45 Bad HELIX record, was skipped: HELIX 72 AH9 PROBnB 6 SERBnB 50 1 45 Bad HELIX record, was skipped: HELIX 73 AI1 PROCnC 6 SERCnC 50 1 45 Bad HELIX record, was skipped: HELIX 74 AI2 PRODnD 6 SERDnD 50 1 45 Bad HELIX record, was skipped: HELIX 75 AI3 PROEnE 6 SEREnE 50 1 45 Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3q_15833/08_2023/8b3q_15833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3q_15833/08_2023/8b3q_15833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3q_15833/08_2023/8b3q_15833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3q_15833/08_2023/8b3q_15833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3q_15833/08_2023/8b3q_15833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3q_15833/08_2023/8b3q_15833.pdb" } resolution = 2.58 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= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 16470 2.51 5 N 3910 2.21 5 O 4565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 25095 Number of models: 1 Model: "" Number of chains: 75 Chain: "AA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Aa" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ba" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ca" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Da" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ea" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ab" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bb" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Cb" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Db" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Eb" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ac" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bc" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Cc" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Dc" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ec" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ad" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bd" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Cd" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Dd" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ed" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ae" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Be" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ce" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "De" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ee" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Af" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bf" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Cf" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Df" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ef" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ag" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "Bg" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "Cg" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "Dg" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "Eg" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "Ah" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bh" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ch" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Dh" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Eh" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ai" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bi" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ci" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Di" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ei" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Aj" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bj" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Cj" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Dj" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ej" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ak" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bk" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ck" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Dk" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Ek" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Al" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bl" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Cl" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Dl" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "El" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Am" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bm" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Cm" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Dm" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Em" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "An" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Bn" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Cn" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Dn" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "En" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 12.24, per 1000 atoms: 0.49 Number of scatterers: 25095 At special positions: 0 Unit cell: (82.59, 80.3876, 298.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4565 8.00 N 3910 7.00 C 16470 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: 9.71 Conformation dependent library (CDL) restraints added in 3.6 seconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6340 Finding SS restraints... Bad HELIX record, was skipped: HELIX 1 AA1 ASPAAA 5 SERAAA 50 1 46 Bad HELIX record, was skipped: HELIX 2 AA2 PROBBB 6 SERBBB 50 1 45 Bad HELIX record, was skipped: HELIX 3 AA3 PROCCC 6 SERCCC 50 1 45 Bad HELIX record, was skipped: HELIX 4 AA4 PRODDD 6 SERDDD 50 1 45 Bad HELIX record, was skipped: HELIX 5 AA5 PROEEE 6 SEREEE 50 1 45 Bad HELIX record, was skipped: HELIX 6 AA6 PROAaA 6 SERAaA 50 1 45 Bad HELIX record, was skipped: HELIX 7 AA7 PROBaB 6 SERBaB 50 1 45 Bad HELIX record, was skipped: HELIX 8 AA8 PROCaC 6 SERCaC 50 1 45 Bad HELIX record, was skipped: HELIX 9 AA9 PRODaD 6 SERDaD 50 1 45 Bad HELIX record, was skipped: HELIX 10 AB1 PROEaE 6 SEREaE 50 1 45 Bad HELIX record, was skipped: HELIX 11 AB2 PROAbA 6 SERAbA 50 1 45 Bad HELIX record, was skipped: HELIX 12 AB3 PROBbB 6 SERBbB 50 1 45 Bad HELIX record, was skipped: HELIX 13 AB4 PROCbC 6 SERCbC 50 1 45 Bad HELIX record, was skipped: HELIX 14 AB5 PRODbD 6 SERDbD 50 1 45 Bad HELIX record, was skipped: HELIX 15 AB6 PROEbE 6 SEREbE 50 1 45 Bad HELIX record, was skipped: HELIX 16 AB7 PROAcA 6 SERAcA 50 1 45 Bad HELIX record, was skipped: HELIX 17 AB8 PROBcB 6 SERBcB 50 1 45 Bad HELIX record, was skipped: HELIX 18 AB9 PROCcC 6 SERCcC 50 1 45 Bad HELIX record, was skipped: HELIX 19 AC1 PRODcD 6 SERDcD 50 1 45 Bad HELIX record, was skipped: HELIX 20 AC2 PROEcE 6 SEREcE 50 1 45 Bad HELIX record, was skipped: HELIX 21 AC3 PROAdA 6 SERAdA 50 1 45 Bad HELIX record, was skipped: HELIX 22 AC4 PROBdB 6 SERBdB 50 1 45 Bad HELIX record, was skipped: HELIX 23 AC5 PROCdC 6 SERCdC 50 1 45 Bad HELIX record, was skipped: HELIX 24 AC6 PRODdD 6 SERDdD 50 1 45 Bad HELIX record, was skipped: HELIX 25 AC7 PROEdE 6 SEREdE 50 1 45 Bad HELIX record, was skipped: HELIX 26 AC8 PROAeA 6 SERAeA 50 1 45 Bad HELIX record, was skipped: HELIX 27 AC9 PROBeB 6 SERBeB 50 1 45 Bad HELIX record, was skipped: HELIX 28 AD1 PROCeC 6 SERCeC 50 1 45 Bad HELIX record, was skipped: HELIX 29 AD2 PRODeD 6 SERDeD 50 1 45 Bad HELIX record, was skipped: HELIX 30 AD3 PROEeE 6 SEREeE 50 1 45 Bad HELIX record, was skipped: HELIX 31 AD4 PROAfA 6 SERAfA 50 1 45 Bad HELIX record, was skipped: HELIX 32 AD5 PROBfB 6 SERBfB 50 1 45 Bad HELIX record, was skipped: HELIX 33 AD6 PROCfC 6 SERCfC 50 1 45 Bad HELIX record, was skipped: HELIX 34 AD7 PRODfD 6 SERDfD 50 1 45 Bad HELIX record, was skipped: HELIX 35 AD8 PROEfE 6 SEREfE 50 1 45 Bad HELIX record, was skipped: HELIX 36 AD9 SERAgA 17 SERAgA 50 1 34 Bad HELIX record, was skipped: HELIX 37 AE1 SERBgB 17 SERBgB 50 1 34 Bad HELIX record, was skipped: HELIX 38 AE2 SERCgC 17 SERCgC 50 1 34 Bad HELIX record, was skipped: HELIX 39 AE3 SERDgD 17 SERDgD 50 1 34 Bad HELIX record, was skipped: HELIX 40 AE4 SEREgE 17 SEREgE 50 1 34 Bad HELIX record, was skipped: HELIX 41 AE5 PROAhA 6 SERAhA 50 1 45 Bad HELIX record, was skipped: HELIX 42 AE6 PROBhB 6 SERBhB 50 1 45 Bad HELIX record, was skipped: HELIX 43 AE7 PROChC 6 SERChC 50 1 45 Bad HELIX record, was skipped: HELIX 44 AE8 PRODhD 6 SERDhD 50 1 45 Bad HELIX record, was skipped: HELIX 45 AE9 PROEhE 6 SEREhE 50 1 45 Bad HELIX record, was skipped: HELIX 46 AF1 PROAiA 6 SERAiA 50 1 45 Bad HELIX record, was skipped: HELIX 47 AF2 PROBiB 6 SERBiB 50 1 45 Bad HELIX record, was skipped: HELIX 48 AF3 PROCiC 6 SERCiC 50 1 45 Bad HELIX record, was skipped: HELIX 49 AF4 PRODiD 6 SERDiD 50 1 45 Bad HELIX record, was skipped: HELIX 50 AF5 PROEiE 6 SEREiE 50 1 45 Bad HELIX record, was skipped: HELIX 51 AF6 PROAjA 6 SERAjA 50 1 45 Bad HELIX record, was skipped: HELIX 52 AF7 PROBjB 6 SERBjB 50 1 45 Bad HELIX record, was skipped: HELIX 53 AF8 PROCjC 6 SERCjC 50 1 45 Bad HELIX record, was skipped: HELIX 54 AF9 PRODjD 6 SERDjD 50 1 45 Bad HELIX record, was skipped: HELIX 55 AG1 PROEjE 6 SEREjE 50 1 45 Bad HELIX record, was skipped: HELIX 56 AG2 PROAkA 6 SERAkA 50 1 45 Bad HELIX record, was skipped: HELIX 57 AG3 PROBkB 6 SERBkB 50 1 45 Bad HELIX record, was skipped: HELIX 58 AG4 PROCkC 6 SERCkC 50 1 45 Bad HELIX record, was skipped: HELIX 59 AG5 PRODkD 6 SERDkD 50 1 45 Bad HELIX record, was skipped: HELIX 60 AG6 PROEkE 6 SEREkE 50 1 45 Bad HELIX record, was skipped: HELIX 61 AG7 PROAlA 6 SERAlA 50 1 45 Bad HELIX record, was skipped: HELIX 62 AG8 PROBlB 6 SERBlB 50 1 45 Bad HELIX record, was skipped: HELIX 63 AG9 PROClC 6 SERClC 50 1 45 Bad HELIX record, was skipped: HELIX 64 AH1 PRODlD 6 SERDlD 50 1 45 Bad HELIX record, was skipped: HELIX 65 AH2 PROElE 6 SERElE 50 1 45 Bad HELIX record, was skipped: HELIX 66 AH3 PROAmA 6 SERAmA 50 1 45 Bad HELIX record, was skipped: HELIX 67 AH4 PROBmB 6 SERBmB 50 1 45 Bad HELIX record, was skipped: HELIX 68 AH5 PROCmC 6 SERCmC 50 1 45 Bad HELIX record, was skipped: HELIX 69 AH6 PRODmD 6 SERDmD 50 1 45 Bad HELIX record, was skipped: HELIX 70 AH7 PROEmE 6 SEREmE 50 1 45 Bad HELIX record, was skipped: HELIX 71 AH8 PROAnA 6 SERAnA 50 1 45 Bad HELIX record, was skipped: HELIX 72 AH9 PROBnB 6 SERBnB 50 1 45 Bad HELIX record, was skipped: HELIX 73 AI1 PROCnC 6 SERCnC 50 1 45 Bad HELIX record, was skipped: HELIX 74 AI2 PRODnD 6 SERDnD 50 1 45 Bad HELIX record, was skipped: HELIX 75 AI3 PROEnE 6 SEREnE 50 1 45 running ksdssp... Secondary structure from input PDB file: 75 helices and 0 sheets defined 95.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'AA' and resid 6 through 49 Processing helix chain 'BB' and resid 6 through 49 Processing helix chain 'CC' and resid 6 through 49 Processing helix chain 'DD' and resid 6 through 49 Processing helix chain 'EE' and resid 6 through 49 Processing helix chain 'Aa' and resid 6 through 49 Processing helix chain 'Ba' and resid 6 through 49 Processing helix chain 'Ca' and resid 6 through 49 Processing helix chain 'Da' and resid 6 through 49 Processing helix chain 'Ea' and resid 6 through 49 Processing helix chain 'Ab' and resid 6 through 49 Processing helix chain 'Bb' and resid 6 through 49 Processing helix chain 'Cb' and resid 6 through 49 Processing helix chain 'Db' and resid 6 through 49 Processing helix chain 'Eb' and resid 6 through 49 Processing helix chain 'Ac' and resid 6 through 49 Processing helix chain 'Bc' and resid 6 through 49 Processing helix chain 'Cc' and resid 6 through 49 Processing helix chain 'Dc' and resid 6 through 49 Processing helix chain 'Ec' and resid 6 through 49 Processing helix chain 'Ad' and resid 6 through 49 Processing helix chain 'Bd' and resid 6 through 49 Processing helix chain 'Cd' and resid 6 through 49 Processing helix chain 'Dd' and resid 6 through 49 Processing helix chain 'Ed' and resid 6 through 49 Processing helix chain 'Ae' and resid 6 through 49 Processing helix chain 'Be' and resid 6 through 49 Processing helix chain 'Ce' and resid 6 through 49 Processing helix chain 'De' and resid 6 through 49 Processing helix chain 'Ee' and resid 6 through 49 Processing helix chain 'Af' and resid 6 through 49 Processing helix chain 'Bf' and resid 6 through 49 Processing helix chain 'Cf' and resid 6 through 49 Processing helix chain 'Df' and resid 6 through 49 Processing helix chain 'Ef' and resid 6 through 49 Processing helix chain 'Ag' and resid 17 through 49 Processing helix chain 'Bg' and resid 17 through 49 Processing helix chain 'Cg' and resid 17 through 49 Processing helix chain 'Dg' and resid 17 through 49 Processing helix chain 'Eg' and resid 17 through 49 Processing helix chain 'Ah' and resid 6 through 49 Processing helix chain 'Bh' and resid 6 through 49 Processing helix chain 'Ch' and resid 6 through 49 Processing helix chain 'Dh' and resid 6 through 49 Processing helix chain 'Eh' and resid 6 through 49 Processing helix chain 'Ai' and resid 6 through 49 Processing helix chain 'Bi' and resid 6 through 49 Processing helix chain 'Ci' and resid 6 through 49 Processing helix chain 'Di' and resid 6 through 49 Processing helix chain 'Ei' and resid 6 through 49 Processing helix chain 'Aj' and resid 6 through 49 Processing helix chain 'Bj' and resid 6 through 49 Processing helix chain 'Cj' and resid 6 through 49 Processing helix chain 'Dj' and resid 6 through 49 Processing helix chain 'Ej' and resid 6 through 49 Processing helix chain 'Ak' and resid 6 through 49 Processing helix chain 'Bk' and resid 6 through 49 Processing helix chain 'Ck' and resid 6 through 49 Processing helix chain 'Dk' and resid 6 through 49 Processing helix chain 'Ek' and resid 6 through 49 Processing helix chain 'Al' and resid 6 through 49 Processing helix chain 'Bl' and resid 6 through 49 Processing helix chain 'Cl' and resid 6 through 49 Processing helix chain 'Dl' and resid 6 through 49 Processing helix chain 'El' and resid 6 through 49 Processing helix chain 'Am' and resid 6 through 49 Processing helix chain 'Bm' and resid 6 through 49 Processing helix chain 'Cm' and resid 6 through 49 Processing helix chain 'Dm' and resid 6 through 49 Processing helix chain 'Em' and resid 6 through 49 Processing helix chain 'An' and resid 6 through 49 Processing helix chain 'Bn' and resid 6 through 49 Processing helix chain 'Cn' and resid 6 through 49 Processing helix chain 'Dn' and resid 6 through 49 Processing helix chain 'En' and resid 6 through 49 2945 hydrogen bonds defined for protein. 8835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.97 Time building geometry restraints manager: 10.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4952 1.33 - 1.45: 7494 1.45 - 1.57: 12789 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 25535 Sorted by residual: bond pdb=" N ALADg 16 " pdb=" CA ALADg 16 " ideal model delta sigma weight residual 1.458 1.533 -0.075 1.90e-02 2.77e+03 1.54e+01 bond pdb=" N ALAAg 16 " pdb=" CA ALAAg 16 " ideal model delta sigma weight residual 1.458 1.532 -0.074 1.90e-02 2.77e+03 1.53e+01 bond pdb=" CA SERCb 47 " pdb=" CB SERCb 47 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.55e-02 4.16e+03 1.51e+01 bond pdb=" CA SEREa 47 " pdb=" CB SEREa 47 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.55e-02 4.16e+03 1.47e+01 bond pdb=" CA SEREc 47 " pdb=" CB SEREc 47 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.55e-02 4.16e+03 1.47e+01 ... (remaining 25530 not shown) Histogram of bond angle deviations from ideal: 96.29 - 104.00: 401 104.00 - 111.72: 10448 111.72 - 119.44: 12302 119.44 - 127.15: 11078 127.15 - 134.87: 231 Bond angle restraints: 34460 Sorted by residual: angle pdb=" CA PHEAc 45 " pdb=" CB PHEAc 45 " pdb=" CG PHEAc 45 " ideal model delta sigma weight residual 113.80 107.56 6.24 1.00e+00 1.00e+00 3.89e+01 angle pdb=" CA PHEAb 45 " pdb=" CB PHEAb 45 " pdb=" CG PHEAb 45 " ideal model delta sigma weight residual 113.80 107.57 6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" CA PHECa 45 " pdb=" CB PHECa 45 " pdb=" CG PHECa 45 " ideal model delta sigma weight residual 113.80 107.63 6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" CA PHEEb 45 " pdb=" CB PHEEb 45 " pdb=" CG PHEEb 45 " ideal model delta sigma weight residual 113.80 107.66 6.14 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CA PHEDc 45 " pdb=" CB PHEDc 45 " pdb=" CG PHEDc 45 " ideal model delta sigma weight residual 113.80 107.68 6.12 1.00e+00 1.00e+00 3.75e+01 ... (remaining 34455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.80: 12575 11.80 - 23.60: 1346 23.60 - 35.40: 835 35.40 - 47.20: 278 47.20 - 59.01: 81 Dihedral angle restraints: 15115 sinusoidal: 5380 harmonic: 9735 Sorted by residual: dihedral pdb=" C THREg 19 " pdb=" N THREg 19 " pdb=" CA THREg 19 " pdb=" CB THREg 19 " ideal model delta harmonic sigma weight residual -122.00 -130.66 8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" CB METEj 28 " pdb=" CG METEj 28 " pdb=" SD METEj 28 " pdb=" CE METEj 28 " ideal model delta sinusoidal sigma weight residual -60.00 -119.01 59.01 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N SERCk 13 " pdb=" CA SERCk 13 " pdb=" CB SERCk 13 " pdb=" OG SERCk 13 " ideal model delta sinusoidal sigma weight residual -60.00 -1.23 -58.77 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 15112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2265 0.064 - 0.128: 1281 0.128 - 0.192: 355 0.192 - 0.257: 180 0.257 - 0.321: 59 Chirality restraints: 4140 Sorted by residual: chirality pdb=" CA PHEDa 45 " pdb=" N PHEDa 45 " pdb=" C PHEDa 45 " pdb=" CB PHEDa 45 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PHEEh 45 " pdb=" N PHEEh 45 " pdb=" C PHEEh 45 " pdb=" CB PHEEh 45 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA PHEAa 45 " pdb=" N PHEAa 45 " pdb=" C PHEAa 45 " pdb=" CB PHEAa 45 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 4137 not shown) Planarity restraints: 4120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRDh 24 " 0.049 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYRDh 24 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYRDh 24 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYRDh 24 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYRDh 24 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYRDh 24 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYRDh 24 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYRDh 24 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYREi 24 " 0.050 2.00e-02 2.50e+03 3.10e-02 1.92e+01 pdb=" CG TYREi 24 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYREi 24 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYREi 24 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYREi 24 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYREi 24 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYREi 24 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYREi 24 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRBB 24 " -0.048 2.00e-02 2.50e+03 3.08e-02 1.90e+01 pdb=" CG TYRBB 24 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYRBB 24 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYRBB 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYRBB 24 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYRBB 24 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYRBB 24 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYRBB 24 " -0.051 2.00e-02 2.50e+03 ... (remaining 4117 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8202 2.86 - 3.37: 28046 3.37 - 3.88: 40893 3.88 - 4.39: 41773 4.39 - 4.90: 73798 Nonbonded interactions: 192712 Sorted by model distance: nonbonded pdb=" NZ LYSEd 40 " pdb=" OXT SEREe 50 " model vdw 2.348 2.520 nonbonded pdb=" NZ LYSEb 40 " pdb=" OXT SEREc 50 " model vdw 2.348 2.520 nonbonded pdb=" NZ LYSDd 40 " pdb=" OXT SERDe 50 " model vdw 2.350 2.520 nonbonded pdb=" NZ LYSBd 40 " pdb=" OXT SERBe 50 " model vdw 2.350 2.520 nonbonded pdb=" NZ LYSCd 40 " pdb=" OXT SERCe 50 " model vdw 2.351 2.520 ... (remaining 192707 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 'AA' selection = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'BB' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' selection = chain 'Bd' selection = chain 'Be' selection = chain 'Bf' selection = chain 'Bh' selection = chain 'Bi' selection = chain 'Bj' selection = chain 'Bk' selection = chain 'Bl' selection = chain 'Bm' selection = chain 'Bn' selection = chain 'CC' selection = chain 'Ca' selection = chain 'Cb' selection = chain 'Cc' selection = chain 'Cd' selection = chain 'Ce' selection = chain 'Cf' selection = chain 'Ch' selection = chain 'Ci' selection = chain 'Cj' selection = chain 'Ck' selection = chain 'Cl' selection = chain 'Cm' selection = chain 'Cn' selection = chain 'DD' selection = chain 'Da' selection = chain 'Db' selection = chain 'Dc' selection = chain 'Dd' selection = chain 'De' selection = chain 'Df' selection = chain 'Dh' selection = chain 'Di' selection = chain 'Dj' selection = chain 'Dk' selection = chain 'Dl' selection = chain 'Dm' selection = chain 'Dn' selection = chain 'EE' selection = chain 'Ea' selection = chain 'Eb' selection = chain 'Ec' selection = chain 'Ed' selection = chain 'Ee' selection = chain 'Ef' selection = chain 'Eh' selection = chain 'Ei' selection = chain 'Ej' selection = chain 'Ek' selection = chain 'El' selection = chain 'Em' selection = chain 'En' } ncs_group { reference = chain 'Ag' selection = chain 'Bg' selection = chain 'Cg' selection = chain 'Dg' selection = chain 'Eg' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.020 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 62.060 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.530 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:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9332 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 : 0.011 0.075 25535 Z= 0.709 Angle : 1.554 8.640 34460 Z= 1.083 Chirality : 0.093 0.321 4140 Planarity : 0.007 0.031 4120 Dihedral : 14.854 59.006 8775 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.12), residues: 3245 helix: -0.53 (0.07), residues: 3245 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1030 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 1035 average time/residue: 1.2748 time to fit residues: 1522.1267 Evaluate side-chains 702 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 697 time to evaluate : 2.823 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 5 average time/residue: 0.3378 time to fit residues: 6.2942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 231 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Be 15 GLN Ce 15 GLN Ee 15 GLN Bf 15 GLN Ef 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 25535 Z= 0.188 Angle : 0.459 4.395 34460 Z= 0.266 Chirality : 0.035 0.114 4140 Planarity : 0.003 0.017 4120 Dihedral : 4.824 30.390 3470 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 5.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.89 (0.11), residues: 3245 helix: 3.19 (0.07), residues: 3095 sheet: None (None), residues: 0 loop : 3.13 (0.12), residues: 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 912 time to evaluate : 3.031 Fit side-chains revert: symmetry clash outliers start: 138 outliers final: 36 residues processed: 975 average time/residue: 1.2502 time to fit residues: 1409.4788 Evaluate side-chains 737 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 701 time to evaluate : 2.976 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 34 residues processed: 2 average time/residue: 0.2063 time to fit residues: 4.4469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 15 GLN Ce 15 GLN Bf 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9248 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 25535 Z= 0.307 Angle : 0.473 5.067 34460 Z= 0.275 Chirality : 0.033 0.102 4140 Planarity : 0.002 0.013 4120 Dihedral : 4.857 40.917 3470 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 4.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.74 (0.11), residues: 3245 helix: 3.78 (0.07), residues: 3095 sheet: None (None), residues: 0 loop : 2.18 (0.25), residues: 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 700 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 52 residues processed: 760 average time/residue: 1.3336 time to fit residues: 1163.7842 Evaluate side-chains 694 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 642 time to evaluate : 2.811 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 46 residues processed: 7 average time/residue: 0.9817 time to fit residues: 11.9077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 128 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 15 GLN Ce 15 GLN Bf 15 GLN Cn 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9254 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 25535 Z= 0.316 Angle : 0.483 6.039 34460 Z= 0.279 Chirality : 0.033 0.099 4140 Planarity : 0.002 0.012 4120 Dihedral : 5.113 49.435 3470 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.84 (0.11), residues: 3245 helix: 3.86 (0.07), residues: 3095 sheet: None (None), residues: 0 loop : 1.76 (0.30), residues: 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 662 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 55 residues processed: 723 average time/residue: 1.4157 time to fit residues: 1168.1308 Evaluate side-chains 684 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 629 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 46 residues processed: 9 average time/residue: 0.8625 time to fit residues: 13.2283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ce 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 25535 Z= 0.164 Angle : 0.438 6.584 34460 Z= 0.244 Chirality : 0.032 0.120 4140 Planarity : 0.002 0.013 4120 Dihedral : 4.027 40.205 3470 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 6.87 (0.11), residues: 3245 helix: 4.45 (0.07), residues: 3095 sheet: None (None), residues: 0 loop : 3.52 (0.25), residues: 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 774 time to evaluate : 2.970 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 outliers start: 91 outliers final: 50 residues processed: 832 average time/residue: 1.2790 time to fit residues: 1233.1553 Evaluate side-chains 673 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 623 time to evaluate : 3.675 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 47 residues processed: 4 average time/residue: 0.6481 time to fit residues: 7.6057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ce 15 GLN En 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 25535 Z= 0.191 Angle : 0.490 7.207 34460 Z= 0.271 Chirality : 0.032 0.126 4140 Planarity : 0.002 0.017 4120 Dihedral : 3.761 38.077 3470 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 6.67 (0.11), residues: 3245 helix: 4.35 (0.07), residues: 3095 sheet: None (None), residues: 0 loop : 2.93 (0.24), residues: 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 642 time to evaluate : 2.987 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 outliers start: 69 outliers final: 47 residues processed: 694 average time/residue: 1.3092 time to fit residues: 1046.5936 Evaluate side-chains 650 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 603 time to evaluate : 2.619 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 44 residues processed: 4 average time/residue: 0.9196 time to fit residues: 7.8091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 240 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 25535 Z= 0.205 Angle : 0.506 7.823 34460 Z= 0.282 Chirality : 0.032 0.128 4140 Planarity : 0.002 0.019 4120 Dihedral : 3.629 36.748 3470 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 6.45 (0.11), residues: 3245 helix: 4.22 (0.07), residues: 3095 sheet: None (None), residues: 0 loop : 2.59 (0.25), residues: 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 616 time to evaluate : 2.841 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 outliers start: 74 outliers final: 52 residues processed: 668 average time/residue: 1.3933 time to fit residues: 1066.7718 Evaluate side-chains 653 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 601 time to evaluate : 3.003 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 45 residues processed: 8 average time/residue: 1.1897 time to fit residues: 14.8529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 140 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 25535 Z= 0.178 Angle : 0.509 8.561 34460 Z= 0.279 Chirality : 0.032 0.142 4140 Planarity : 0.002 0.022 4120 Dihedral : 3.236 27.576 3470 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 6.62 (0.11), residues: 3245 helix: 4.32 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 2.57 (0.17), residues: 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 671 time to evaluate : 2.769 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: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 52 residues processed: 717 average time/residue: 1.2941 time to fit residues: 1072.0404 Evaluate side-chains 687 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 635 time to evaluate : 2.956 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 45 residues processed: 8 average time/residue: 1.1530 time to fit residues: 14.5367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 264 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 208 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 25535 Z= 0.185 Angle : 0.529 9.034 34460 Z= 0.292 Chirality : 0.033 0.148 4140 Planarity : 0.002 0.023 4120 Dihedral : 3.126 23.297 3470 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 6.53 (0.11), residues: 3245 helix: 4.27 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 2.44 (0.19), residues: 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 640 time to evaluate : 3.016 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 outliers start: 60 outliers final: 49 residues processed: 686 average time/residue: 1.3366 time to fit residues: 1059.6757 Evaluate side-chains 668 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 619 time to evaluate : 2.969 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 45 residues processed: 5 average time/residue: 1.1228 time to fit residues: 10.2562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9222 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 25535 Z= 0.308 Angle : 0.592 9.790 34460 Z= 0.337 Chirality : 0.035 0.157 4140 Planarity : 0.003 0.035 4120 Dihedral : 3.310 31.681 3470 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.70 (0.12), residues: 3245 helix: 3.79 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 0.87 (0.17), residues: 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 634 time to evaluate : 3.091 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 outliers start: 64 outliers final: 46 residues processed: 681 average time/residue: 1.2943 time to fit residues: 1015.5624 Evaluate side-chains 648 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 602 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 44 residues processed: 2 average time/residue: 1.2729 time to fit residues: 6.9329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Dn 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.065491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.044966 restraints weight = 66296.896| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.53 r_work: 0.2836 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 25535 Z= 0.190 Angle : 0.558 9.541 34460 Z= 0.311 Chirality : 0.034 0.194 4140 Planarity : 0.003 0.036 4120 Dihedral : 3.201 26.007 3470 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 6.19 (0.11), residues: 3245 helix: 4.07 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 1.94 (0.21), residues: 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14495.96 seconds wall clock time: 255 minutes 15.24 seconds (15315.24 seconds total)