Starting phenix.real_space_refine on Thu Aug 8 05:26:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tob_41442/08_2024/8tob_41442.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tob_41442/08_2024/8tob_41442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tob_41442/08_2024/8tob_41442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tob_41442/08_2024/8tob_41442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tob_41442/08_2024/8tob_41442.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tob_41442/08_2024/8tob_41442.cif" } resolution = 3.14 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= 0.010 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 132 5.16 5 C 14014 2.51 5 N 3674 2.21 5 O 4422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "GA GLU 55": "OE1" <-> "OE2" Residue "HA GLU 12": "OE1" <-> "OE2" Residue "HA TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA GLU 46": "OE1" <-> "OE2" Residue "HA GLU 68": "OE1" <-> "OE2" Residue "IA GLU 55": "OE1" <-> "OE2" Residue "JA GLU 55": "OE1" <-> "OE2" Residue "KA GLU 68": "OE1" <-> "OE2" Residue "LA GLU 12": "OE1" <-> "OE2" Residue "LA TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 55": "OE1" <-> "OE2" Residue "LA ASP 60": "OD1" <-> "OD2" Residue "MA TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA ASP 60": "OD1" <-> "OD2" Residue "NA TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA ASP 60": "OD1" <-> "OD2" Residue "NA GLU 68": "OE1" <-> "OE2" Residue "PA GLU 12": "OE1" <-> "OE2" Residue "PA ASP 60": "OD1" <-> "OD2" Residue "QA GLU 68": "OE1" <-> "OE2" Residue "RA GLU 55": "OE1" <-> "OE2" Residue "RA ASP 60": "OD1" <-> "OD2" Residue "SA GLU 55": "OE1" <-> "OE2" Residue "SA ASP 60": "OD1" <-> "OD2" Residue "TA GLU 46": "OE1" <-> "OE2" Residue "TA GLU 55": "OE1" <-> "OE2" Residue "TA ASP 60": "OD1" <-> "OD2" Residue "TA GLU 68": "OE1" <-> "OE2" Residue "UA ASP 60": "OD1" <-> "OD2" Residue "UA GLU 68": "OE1" <-> "OE2" Residue "VA GLU 12": "OE1" <-> "OE2" Residue "VA GLU 55": "OE1" <-> "OE2" Residue "VA ASP 60": "OD1" <-> "OD2" Residue "AA GLU 12": "OE1" <-> "OE2" Residue "AA TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA GLU 55": "OE1" <-> "OE2" Residue "AA ASP 60": "OD1" <-> "OD2" Residue "AA GLU 68": "OE1" <-> "OE2" Residue "BA GLU 12": "OE1" <-> "OE2" Residue "BA TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 46": "OE1" <-> "OE2" Residue "BA ASP 60": "OD1" <-> "OD2" Residue "CA GLU 12": "OE1" <-> "OE2" Residue "CA TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA ASP 60": "OD1" <-> "OD2" Residue "DA GLU 55": "OE1" <-> "OE2" Residue "DA ASP 60": "OD1" <-> "OD2" Residue "DA GLU 68": "OE1" <-> "OE2" Residue "EA GLU 12": "OE1" <-> "OE2" Residue "EA ASP 60": "OD1" <-> "OD2" Residue "EA GLU 68": "OE1" <-> "OE2" Residue "FA TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA ASP 60": "OD1" <-> "OD2" Residue "GB GLU 127": "OE1" <-> "OE2" Residue "GB GLU 137": "OE1" <-> "OE2" Residue "IB GLU 99": "OE1" <-> "OE2" Residue "JB GLU 99": "OE1" <-> "OE2" Residue "LB GLU 137": "OE1" <-> "OE2" Residue "MB GLU 127": "OE1" <-> "OE2" Residue "NB GLU 99": "OE1" <-> "OE2" Residue "NB GLU 127": "OE1" <-> "OE2" Residue "OB GLU 99": "OE1" <-> "OE2" Residue "OB GLU 127": "OE1" <-> "OE2" Residue "QB GLU 99": "OE1" <-> "OE2" Residue "QB GLU 127": "OE1" <-> "OE2" Residue "RB GLU 137": "OE1" <-> "OE2" Residue "SB GLU 137": "OE1" <-> "OE2" Residue "UB GLU 127": "OE1" <-> "OE2" Residue "VB GLU 99": "OE1" <-> "OE2" Residue "AB GLU 137": "OE1" <-> "OE2" Residue "BB GLU 127": "OE1" <-> "OE2" Residue "CB GLU 99": "OE1" <-> "OE2" Residue "DB GLU 137": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 22242 Number of models: 1 Model: "" Number of chains: 44 Chain: "GA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "HA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "IA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "JA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "KA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "LA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "MA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "NA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "OA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "PA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "QA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "RA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "SA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "TA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "UA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "VA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "AA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "BA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "CA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "DA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "EA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "FA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "GB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "HB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "IB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "JB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "KB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "LB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "MB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "NB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "OB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "PB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "QB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "RB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "SB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "TB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "UB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "VB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "AB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "BB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "CB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "DB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "EB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "FB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Time building chain proxies: 13.10, per 1000 atoms: 0.59 Number of scatterers: 22242 At special positions: 0 Unit cell: (74.048, 74.048, 307.84, 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 132 16.00 O 4422 8.00 N 3674 7.00 C 14014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYSGA 57 " - pdb=" SG CYSGA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSHA 57 " - pdb=" SG CYSHA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSIA 57 " - pdb=" SG CYSIA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSJA 57 " - pdb=" SG CYSJA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSKA 57 " - pdb=" SG CYSKA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSLA 57 " - pdb=" SG CYSLA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSMA 57 " - pdb=" SG CYSMA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSNA 57 " - pdb=" SG CYSNA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSOA 57 " - pdb=" SG CYSOA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSPA 57 " - pdb=" SG CYSPA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSQA 57 " - pdb=" SG CYSQA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSRA 57 " - pdb=" SG CYSRA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSSA 57 " - pdb=" SG CYSSA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSTA 57 " - pdb=" SG CYSTA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSUA 57 " - pdb=" SG CYSUA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSVA 57 " - pdb=" SG CYSVA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 57 " - pdb=" SG CYSAA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSBA 57 " - pdb=" SG CYSBA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSCA 57 " - pdb=" SG CYSCA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSDA 57 " - pdb=" SG CYSDA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSEA 57 " - pdb=" SG CYSEA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSFA 57 " - pdb=" SG CYSFA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSGB 132 " - pdb=" SG CYSGB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSHB 132 " - pdb=" SG CYSHB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSIB 132 " - pdb=" SG CYSIB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSJB 132 " - pdb=" SG CYSJB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSKB 132 " - pdb=" SG CYSKB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSLB 132 " - pdb=" SG CYSLB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSMB 132 " - pdb=" SG CYSMB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSNB 132 " - pdb=" SG CYSNB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSOB 132 " - pdb=" SG CYSOB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSPB 132 " - pdb=" SG CYSPB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSQB 132 " - pdb=" SG CYSQB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSRB 132 " - pdb=" SG CYSRB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSSB 132 " - pdb=" SG CYSSB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSTB 132 " - pdb=" SG CYSTB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSUB 132 " - pdb=" SG CYSUB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSVB 132 " - pdb=" SG CYSVB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSAB 132 " - pdb=" SG CYSAB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSBB 132 " - pdb=" SG CYSBB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSCB 132 " - pdb=" SG CYSCB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSDB 132 " - pdb=" SG CYSDB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSEB 132 " - pdb=" SG CYSEB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSFB 132 " - pdb=" SG CYSFB 145 " distance=2.03 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: 8.94 Conformation dependent library (CDL) restraints added in 4.1 seconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 22 sheets defined 39.1% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'GA' and resid 9 through 25 Processing helix chain 'GA' and resid 31 through 49 Processing helix chain 'GA' and resid 50 through 61 Processing helix chain 'HA' and resid 10 through 25 Processing helix chain 'HA' and resid 31 through 50 removed outlier: 3.572A pdb=" N LEUHA 50 " --> pdb=" O GLUHA 46 " (cutoff:3.500A) Processing helix chain 'HA' and resid 50 through 61 Processing helix chain 'IA' and resid 10 through 25 Processing helix chain 'IA' and resid 31 through 49 Processing helix chain 'IA' and resid 50 through 61 Processing helix chain 'JA' and resid 10 through 25 Processing helix chain 'JA' and resid 31 through 49 removed outlier: 3.528A pdb=" N ILEJA 35 " --> pdb=" O TYRJA 31 " (cutoff:3.500A) Processing helix chain 'JA' and resid 50 through 61 Processing helix chain 'KA' and resid 10 through 25 Processing helix chain 'KA' and resid 31 through 49 Processing helix chain 'KA' and resid 50 through 60 Processing helix chain 'LA' and resid 10 through 25 Processing helix chain 'LA' and resid 31 through 59 removed outlier: 3.578A pdb=" N LYSLA 37 " --> pdb=" O ASNLA 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLYLA 48 " --> pdb=" O METLA 44 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEULA 50 " --> pdb=" O GLULA 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYSLA 51 " --> pdb=" O THRLA 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THRLA 52 " --> pdb=" O GLYLA 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VALLA 53 " --> pdb=" O SERLA 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THRLA 56 " --> pdb=" O THRLA 52 " (cutoff:3.500A) Processing helix chain 'MA' and resid 10 through 25 Processing helix chain 'MA' and resid 31 through 49 Processing helix chain 'MA' and resid 50 through 61 Processing helix chain 'NA' and resid 10 through 25 Processing helix chain 'NA' and resid 31 through 59 removed outlier: 3.544A pdb=" N LYSNA 37 " --> pdb=" O ASNNA 33 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLYNA 48 " --> pdb=" O METNA 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEUNA 50 " --> pdb=" O GLUNA 46 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYSNA 51 " --> pdb=" O THRNA 47 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THRNA 52 " --> pdb=" O GLYNA 48 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VALNA 53 " --> pdb=" O SERNA 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THRNA 56 " --> pdb=" O THRNA 52 " (cutoff:3.500A) Processing helix chain 'OA' and resid 10 through 25 Processing helix chain 'OA' and resid 31 through 49 Processing helix chain 'OA' and resid 50 through 60 Processing helix chain 'PA' and resid 10 through 25 removed outlier: 3.629A pdb=" N METPA 14 " --> pdb=" O LEUPA 10 " (cutoff:3.500A) Processing helix chain 'PA' and resid 31 through 49 Processing helix chain 'PA' and resid 50 through 61 Processing helix chain 'QA' and resid 10 through 25 Processing helix chain 'QA' and resid 31 through 49 Processing helix chain 'QA' and resid 50 through 61 Processing helix chain 'RA' and resid 10 through 25 Processing helix chain 'RA' and resid 31 through 59 removed outlier: 3.540A pdb=" N LYSRA 37 " --> pdb=" O ASNRA 33 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEURA 50 " --> pdb=" O GLURA 46 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYSRA 51 " --> pdb=" O THRRA 47 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THRRA 52 " --> pdb=" O GLYRA 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VALRA 53 " --> pdb=" O SERRA 49 " (cutoff:3.500A) Processing helix chain 'SA' and resid 10 through 25 Processing helix chain 'SA' and resid 31 through 49 removed outlier: 3.562A pdb=" N ILESA 35 " --> pdb=" O TYRSA 31 " (cutoff:3.500A) Processing helix chain 'SA' and resid 50 through 61 Processing helix chain 'TA' and resid 10 through 25 Processing helix chain 'TA' and resid 31 through 49 Processing helix chain 'TA' and resid 50 through 61 Processing helix chain 'UA' and resid 10 through 25 Processing helix chain 'UA' and resid 31 through 49 Processing helix chain 'UA' and resid 50 through 61 Processing helix chain 'UA' and resid 74 through 78 removed outlier: 3.813A pdb=" N GLYUA 78 " --> pdb=" O ASNUA 75 " (cutoff:3.500A) Processing helix chain 'VA' and resid 10 through 25 Processing helix chain 'VA' and resid 31 through 49 Processing helix chain 'VA' and resid 50 through 61 Processing helix chain 'AA' and resid 10 through 25 Processing helix chain 'AA' and resid 31 through 50 removed outlier: 3.890A pdb=" N LEUAA 50 " --> pdb=" O GLUAA 46 " (cutoff:3.500A) Processing helix chain 'AA' and resid 50 through 61 Processing helix chain 'BA' and resid 10 through 25 Processing helix chain 'BA' and resid 31 through 49 Processing helix chain 'BA' and resid 50 through 61 Processing helix chain 'CA' and resid 10 through 25 Processing helix chain 'CA' and resid 31 through 49 Processing helix chain 'CA' and resid 50 through 61 Processing helix chain 'DA' and resid 10 through 25 Processing helix chain 'DA' and resid 31 through 49 removed outlier: 3.509A pdb=" N ILEDA 35 " --> pdb=" O TYRDA 31 " (cutoff:3.500A) Processing helix chain 'DA' and resid 50 through 61 Processing helix chain 'EA' and resid 10 through 25 Processing helix chain 'EA' and resid 31 through 59 removed outlier: 3.676A pdb=" N LYSEA 37 " --> pdb=" O ASNEA 33 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEUEA 50 " --> pdb=" O GLUEA 46 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSEA 51 " --> pdb=" O THREA 47 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THREA 52 " --> pdb=" O GLYEA 48 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VALEA 53 " --> pdb=" O SEREA 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THREA 56 " --> pdb=" O THREA 52 " (cutoff:3.500A) Processing helix chain 'FA' and resid 10 through 25 Processing helix chain 'FA' and resid 31 through 49 Processing helix chain 'FA' and resid 50 through 61 Processing helix chain 'GB' and resid 112 through 116 Processing helix chain 'GB' and resid 137 through 141 Processing helix chain 'GB' and resid 142 through 146 removed outlier: 4.133A pdb=" N ALAGB 146 " --> pdb=" O ALAGB 143 " (cutoff:3.500A) Processing helix chain 'HB' and resid 137 through 141 Processing helix chain 'HB' and resid 142 through 146 removed outlier: 3.852A pdb=" N ALAHB 146 " --> pdb=" O ALAHB 143 " (cutoff:3.500A) Processing helix chain 'IB' and resid 137 through 141 Processing helix chain 'IB' and resid 142 through 146 removed outlier: 3.858A pdb=" N ALAIB 146 " --> pdb=" O ALAIB 143 " (cutoff:3.500A) Processing helix chain 'JB' and resid 137 through 141 Processing helix chain 'KB' and resid 137 through 141 Processing helix chain 'KB' and resid 142 through 146 removed outlier: 4.164A pdb=" N ALAKB 146 " --> pdb=" O ALAKB 143 " (cutoff:3.500A) Processing helix chain 'LB' and resid 137 through 141 Processing helix chain 'LB' and resid 142 through 146 removed outlier: 4.039A pdb=" N ALALB 146 " --> pdb=" O ALALB 143 " (cutoff:3.500A) Processing helix chain 'MB' and resid 137 through 141 Processing helix chain 'NB' and resid 137 through 141 Processing helix chain 'OB' and resid 137 through 141 Processing helix chain 'PB' and resid 137 through 141 Processing helix chain 'PB' and resid 142 through 146 removed outlier: 4.061A pdb=" N ALAPB 146 " --> pdb=" O ALAPB 143 " (cutoff:3.500A) Processing helix chain 'QB' and resid 137 through 141 Processing helix chain 'RB' and resid 137 through 141 Processing helix chain 'SB' and resid 142 through 146 removed outlier: 4.003A pdb=" N ALASB 146 " --> pdb=" O ALASB 143 " (cutoff:3.500A) Processing helix chain 'TB' and resid 137 through 141 Processing helix chain 'TB' and resid 142 through 146 removed outlier: 3.694A pdb=" N ALATB 146 " --> pdb=" O ALATB 143 " (cutoff:3.500A) Processing helix chain 'UB' and resid 137 through 141 Processing helix chain 'UB' and resid 142 through 146 removed outlier: 4.093A pdb=" N ALAUB 146 " --> pdb=" O ALAUB 143 " (cutoff:3.500A) Processing helix chain 'VB' and resid 137 through 141 Processing helix chain 'AB' and resid 137 through 141 Processing helix chain 'AB' and resid 142 through 146 removed outlier: 3.782A pdb=" N ALAAB 146 " --> pdb=" O ALAAB 143 " (cutoff:3.500A) Processing helix chain 'BB' and resid 137 through 141 Processing helix chain 'BB' and resid 142 through 146 removed outlier: 4.146A pdb=" N ALABB 146 " --> pdb=" O ALABB 143 " (cutoff:3.500A) Processing helix chain 'CB' and resid 137 through 141 Processing helix chain 'DB' and resid 137 through 141 Processing helix chain 'EB' and resid 142 through 146 removed outlier: 3.711A pdb=" N ALAEB 146 " --> pdb=" O ALAEB 143 " (cutoff:3.500A) Processing helix chain 'FB' and resid 142 through 146 removed outlier: 3.983A pdb=" N ALAFB 146 " --> pdb=" O ALAFB 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'GB' and resid 89 through 92 Processing sheet with id=AA2, first strand: chain 'HB' and resid 89 through 92 Processing sheet with id=AA3, first strand: chain 'IB' and resid 89 through 92 Processing sheet with id=AA4, first strand: chain 'JB' and resid 89 through 92 Processing sheet with id=AA5, first strand: chain 'KB' and resid 89 through 92 Processing sheet with id=AA6, first strand: chain 'LB' and resid 89 through 92 Processing sheet with id=AA7, first strand: chain 'MB' and resid 89 through 92 Processing sheet with id=AA8, first strand: chain 'NB' and resid 89 through 92 Processing sheet with id=AA9, first strand: chain 'OB' and resid 89 through 92 Processing sheet with id=AB1, first strand: chain 'PB' and resid 89 through 92 Processing sheet with id=AB2, first strand: chain 'QB' and resid 89 through 92 Processing sheet with id=AB3, first strand: chain 'RB' and resid 89 through 92 Processing sheet with id=AB4, first strand: chain 'SB' and resid 89 through 92 Processing sheet with id=AB5, first strand: chain 'TB' and resid 89 through 92 Processing sheet with id=AB6, first strand: chain 'UB' and resid 89 through 92 Processing sheet with id=AB7, first strand: chain 'VB' and resid 89 through 92 Processing sheet with id=AB8, first strand: chain 'AB' and resid 89 through 92 Processing sheet with id=AB9, first strand: chain 'BB' and resid 89 through 92 Processing sheet with id=AC1, first strand: chain 'CB' and resid 89 through 92 Processing sheet with id=AC2, first strand: chain 'DB' and resid 89 through 92 Processing sheet with id=AC3, first strand: chain 'EB' and resid 89 through 92 Processing sheet with id=AC4, first strand: chain 'FB' and resid 89 through 92 1110 hydrogen bonds defined for protein. 3102 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: 6.68 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7106 1.34 - 1.46: 5025 1.46 - 1.58: 10221 1.58 - 1.70: 0 1.70 - 1.81: 176 Bond restraints: 22528 Sorted by residual: bond pdb=" CB METVA 14 " pdb=" CG METVA 14 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" SD METVA 14 " pdb=" CE METVA 14 " ideal model delta sigma weight residual 1.791 1.772 0.019 2.50e-02 1.60e+03 5.72e-01 bond pdb=" CA ILEEB 115 " pdb=" C ILEEB 115 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.12e-02 7.97e+03 4.84e-01 bond pdb=" CB METEA 14 " pdb=" CG METEA 14 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.15e-01 bond pdb=" CA ASPFA 60 " pdb=" CB ASPFA 60 " ideal model delta sigma weight residual 1.529 1.540 -0.010 1.63e-02 3.76e+03 4.04e-01 ... (remaining 22523 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 491 107.08 - 113.81: 13754 113.81 - 120.54: 7986 120.54 - 127.27: 8269 127.27 - 134.00: 212 Bond angle restraints: 30712 Sorted by residual: angle pdb=" CB METVA 14 " pdb=" CG METVA 14 " pdb=" SD METVA 14 " ideal model delta sigma weight residual 112.70 100.35 12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C GLYEB 108 " pdb=" N ASNEB 109 " pdb=" CA ASNEB 109 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.96e+00 angle pdb=" CB METEA 14 " pdb=" CG METEA 14 " pdb=" SD METEA 14 " ideal model delta sigma weight residual 112.70 120.83 -8.13 3.00e+00 1.11e-01 7.34e+00 angle pdb=" CB METFA 14 " pdb=" CG METFA 14 " pdb=" SD METFA 14 " ideal model delta sigma weight residual 112.70 120.60 -7.90 3.00e+00 1.11e-01 6.93e+00 angle pdb=" N LEUFA 10 " pdb=" CA LEUFA 10 " pdb=" C LEUFA 10 " ideal model delta sigma weight residual 113.55 110.46 3.09 1.26e+00 6.30e-01 6.02e+00 ... (remaining 30707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12506 17.81 - 35.61: 836 35.61 - 53.42: 169 53.42 - 71.22: 28 71.22 - 89.03: 35 Dihedral angle restraints: 13574 sinusoidal: 4862 harmonic: 8712 Sorted by residual: dihedral pdb=" CA ASNTA 75 " pdb=" C ASNTA 75 " pdb=" N LEUTA 76 " pdb=" CA LEUTA 76 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASNEA 75 " pdb=" C ASNEA 75 " pdb=" N LEUEA 76 " pdb=" CA LEUEA 76 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASNNA 75 " pdb=" C ASNNA 75 " pdb=" N LEUNA 76 " pdb=" CA LEUNA 76 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 13571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2861 0.039 - 0.077: 858 0.077 - 0.116: 149 0.116 - 0.155: 47 0.155 - 0.194: 1 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CA METVA 14 " pdb=" N METVA 14 " pdb=" C METVA 14 " pdb=" CB METVA 14 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA ILEVB 103 " pdb=" N ILEVB 103 " pdb=" C ILEVB 103 " pdb=" CB ILEVB 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILETB 103 " pdb=" N ILETB 103 " pdb=" C ILETB 103 " pdb=" CB ILETB 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 3913 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILEBA 28 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PROBA 29 " -0.071 5.00e-02 4.00e+02 pdb=" CA PROBA 29 " 0.021 5.00e-02 4.00e+02 pdb=" CD PROBA 29 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILERA 28 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRORA 29 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRORA 29 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRORA 29 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEEA 28 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PROEA 29 " -0.060 5.00e-02 4.00e+02 pdb=" CA PROEA 29 " 0.018 5.00e-02 4.00e+02 pdb=" CD PROEA 29 " 0.019 5.00e-02 4.00e+02 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1447 2.74 - 3.28: 23460 3.28 - 3.82: 35640 3.82 - 4.36: 45377 4.36 - 4.90: 77620 Nonbonded interactions: 183544 Sorted by model distance: nonbonded pdb=" O GLULA 46 " pdb=" OG SERLA 49 " model vdw 2.194 3.040 nonbonded pdb=" OG SERCB 79 " pdb=" N THRCB 80 " model vdw 2.206 3.120 nonbonded pdb=" O GLUQA 46 " pdb=" OG SERQA 49 " model vdw 2.219 3.040 nonbonded pdb=" O GLUEA 46 " pdb=" OG SEREA 49 " model vdw 2.226 3.040 nonbonded pdb=" O GLUFA 46 " pdb=" OG SERFA 49 " model vdw 2.229 3.040 ... (remaining 183539 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 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'EA' selection = chain 'FA' selection = chain 'GA' selection = chain 'HA' selection = chain 'IA' selection = chain 'JA' selection = chain 'KA' selection = chain 'LA' selection = chain 'MA' selection = chain 'NA' selection = chain 'OA' selection = chain 'PA' selection = chain 'QA' selection = chain 'RA' selection = chain 'SA' selection = chain 'TA' selection = chain 'UA' selection = chain 'VA' } ncs_group { reference = chain 'AB' selection = chain 'BB' selection = chain 'CB' selection = chain 'DB' selection = chain 'EB' selection = chain 'FB' selection = chain 'GB' selection = chain 'HB' selection = chain 'IB' selection = chain 'JB' selection = chain 'KB' selection = chain 'LB' selection = chain 'MB' selection = chain 'NB' selection = chain 'OB' selection = chain 'PB' selection = chain 'QB' selection = chain 'RB' selection = chain 'SB' selection = chain 'TB' selection = chain 'UB' selection = chain 'VB' } 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: 5.670 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: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 60.100 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 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 : 0.002 0.030 22528 Z= 0.125 Angle : 0.449 12.346 30712 Z= 0.249 Chirality : 0.038 0.194 3916 Planarity : 0.003 0.041 3784 Dihedral : 13.684 89.030 7810 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: 0.69 (0.14), residues: 2970 helix: 1.83 (0.15), residues: 1012 sheet: 0.20 (0.19), residues: 660 loop : -0.46 (0.15), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPQB 122 PHE 0.004 0.000 PHEOB 140 TYR 0.008 0.001 TYRCA 34 ARG 0.004 0.000 ARGBA 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 2.791 Fit side-chains REVERT: MA 60 ASP cc_start: 0.8382 (t70) cc_final: 0.7984 (t0) REVERT: MA 68 GLU cc_start: 0.8599 (tp30) cc_final: 0.8263 (tp30) REVERT: TA 68 GLU cc_start: 0.8660 (tp30) cc_final: 0.8252 (tp30) REVERT: KB 116 LYS cc_start: 0.9188 (tptm) cc_final: 0.8970 (tppt) REVERT: PB 147 SER cc_start: 0.8203 (m) cc_final: 0.7838 (t) REVERT: TB 127 GLU cc_start: 0.8595 (mp0) cc_final: 0.8320 (mp0) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.3252 time to fit residues: 302.8371 Evaluate side-chains 526 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 120 optimal weight: 0.0170 chunk 74 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 115 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 259 optimal weight: 6.9990 overall best weight: 1.4820 ------------------------------------------------------------------------------- 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: 0.9167 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22528 Z= 0.205 Angle : 0.468 7.262 30712 Z= 0.252 Chirality : 0.040 0.167 3916 Planarity : 0.004 0.048 3784 Dihedral : 4.162 52.655 3146 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 0.63 % Allowed : 7.20 % Favored : 92.17 % 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: 0.98 (0.15), residues: 2970 helix: 2.17 (0.16), residues: 1056 sheet: 0.15 (0.19), residues: 660 loop : -0.34 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAB 122 PHE 0.005 0.001 PHEEB 140 TYR 0.008 0.001 TYRIA 34 ARG 0.004 0.000 ARGBA 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 525 time to evaluate : 2.448 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8383 (t70) cc_final: 0.8083 (t0) REVERT: IA 56 THR cc_start: 0.9309 (p) cc_final: 0.9107 (p) REVERT: LA 55 GLU cc_start: 0.9206 (tp30) cc_final: 0.8931 (tp30) REVERT: LA 60 ASP cc_start: 0.8626 (t70) cc_final: 0.8047 (t0) REVERT: MA 60 ASP cc_start: 0.8433 (t70) cc_final: 0.8057 (t0) REVERT: NA 60 ASP cc_start: 0.8345 (t0) cc_final: 0.8133 (t0) REVERT: PA 60 ASP cc_start: 0.8436 (t70) cc_final: 0.8234 (t0) REVERT: QA 60 ASP cc_start: 0.8272 (t70) cc_final: 0.8070 (t0) REVERT: TA 68 GLU cc_start: 0.8706 (tp30) cc_final: 0.8418 (tp30) REVERT: BA 55 GLU cc_start: 0.9162 (tp30) cc_final: 0.8938 (tp30) REVERT: KB 116 LYS cc_start: 0.9211 (tptm) cc_final: 0.8979 (tppt) REVERT: PB 147 SER cc_start: 0.8215 (m) cc_final: 0.7805 (t) REVERT: TB 127 GLU cc_start: 0.8602 (mp0) cc_final: 0.8305 (mp0) outliers start: 15 outliers final: 11 residues processed: 528 average time/residue: 0.3200 time to fit residues: 263.4656 Evaluate side-chains 517 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 506 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 35 ILE Chi-restraints excluded: chain HA residue 52 THR Chi-restraints excluded: chain HA residue 53 VAL Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain KA residue 69 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 14 MET Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain EB residue 147 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 216 optimal weight: 7.9990 chunk 176 optimal weight: 0.0770 chunk 71 optimal weight: 0.0870 chunk 260 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 208 optimal weight: 0.0970 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: HB 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22528 Z= 0.107 Angle : 0.424 6.560 30712 Z= 0.228 Chirality : 0.038 0.150 3916 Planarity : 0.003 0.041 3784 Dihedral : 3.920 45.294 3146 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 0.72 % Allowed : 8.92 % Favored : 90.36 % 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: 1.10 (0.15), residues: 2970 helix: 2.33 (0.16), residues: 1056 sheet: 0.06 (0.19), residues: 638 loop : -0.23 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPQB 122 PHE 0.004 0.000 PHEHB 107 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGRB 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 575 time to evaluate : 2.407 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8322 (t70) cc_final: 0.8044 (t0) REVERT: HA 75 ASN cc_start: 0.9230 (t0) cc_final: 0.9008 (t0) REVERT: IA 56 THR cc_start: 0.9460 (p) cc_final: 0.9257 (p) REVERT: LA 60 ASP cc_start: 0.8610 (t70) cc_final: 0.7955 (t0) REVERT: MA 55 GLU cc_start: 0.9272 (tp30) cc_final: 0.8832 (tp30) REVERT: MA 60 ASP cc_start: 0.8430 (t70) cc_final: 0.8030 (t0) REVERT: NA 55 GLU cc_start: 0.9277 (tp30) cc_final: 0.8760 (tp30) REVERT: OA 60 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8158 (t0) REVERT: PA 60 ASP cc_start: 0.8439 (t70) cc_final: 0.8077 (t0) REVERT: QA 60 ASP cc_start: 0.8279 (t70) cc_final: 0.8042 (t0) REVERT: QA 68 GLU cc_start: 0.8713 (tp30) cc_final: 0.8460 (tp30) REVERT: TA 68 GLU cc_start: 0.8702 (tp30) cc_final: 0.8299 (tp30) REVERT: BA 55 GLU cc_start: 0.9141 (tp30) cc_final: 0.8936 (tp30) REVERT: HB 124 ARG cc_start: 0.8964 (ttt-90) cc_final: 0.8733 (ttt-90) REVERT: KB 116 LYS cc_start: 0.9168 (tptm) cc_final: 0.8959 (tppt) REVERT: PB 147 SER cc_start: 0.8202 (m) cc_final: 0.7797 (t) REVERT: TB 127 GLU cc_start: 0.8567 (mp0) cc_final: 0.8308 (mp0) outliers start: 17 outliers final: 7 residues processed: 579 average time/residue: 0.3178 time to fit residues: 286.5498 Evaluate side-chains 543 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 535 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 35 ILE Chi-restraints excluded: chain HA residue 53 VAL Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 73 ASN Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain TA residue 14 MET Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: KA 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22528 Z= 0.195 Angle : 0.455 7.828 30712 Z= 0.244 Chirality : 0.039 0.151 3916 Planarity : 0.003 0.044 3784 Dihedral : 4.051 40.431 3146 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 0.72 % Allowed : 11.32 % Favored : 87.96 % 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: 1.11 (0.15), residues: 2970 helix: 2.29 (0.16), residues: 1056 sheet: 0.21 (0.19), residues: 660 loop : -0.27 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPRB 122 PHE 0.004 0.001 PHEPB 140 TYR 0.011 0.001 TYRIA 34 ARG 0.001 0.000 ARGMA 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 516 time to evaluate : 2.691 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8349 (t70) cc_final: 0.8062 (t0) REVERT: LA 60 ASP cc_start: 0.8652 (t70) cc_final: 0.7991 (t0) REVERT: MA 55 GLU cc_start: 0.9303 (tp30) cc_final: 0.8779 (tp30) REVERT: MA 60 ASP cc_start: 0.8441 (t70) cc_final: 0.8027 (t0) REVERT: OA 60 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8132 (t0) REVERT: PA 60 ASP cc_start: 0.8460 (t70) cc_final: 0.8083 (t0) REVERT: QA 60 ASP cc_start: 0.8288 (t70) cc_final: 0.8041 (t0) REVERT: QA 68 GLU cc_start: 0.8720 (tp30) cc_final: 0.8464 (tp30) REVERT: TA 68 GLU cc_start: 0.8732 (tp30) cc_final: 0.8443 (tp30) REVERT: BA 55 GLU cc_start: 0.9153 (tp30) cc_final: 0.8911 (tp30) REVERT: HB 124 ARG cc_start: 0.8964 (ttt-90) cc_final: 0.8727 (ttt-90) REVERT: IB 109 ASN cc_start: 0.8846 (t0) cc_final: 0.8386 (t0) REVERT: PB 147 SER cc_start: 0.8178 (m) cc_final: 0.7745 (t) REVERT: TB 127 GLU cc_start: 0.8597 (mp0) cc_final: 0.8297 (mp0) outliers start: 17 outliers final: 9 residues processed: 522 average time/residue: 0.3030 time to fit residues: 248.2303 Evaluate side-chains 514 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 504 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain HA residue 35 ILE Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain RA residue 45 SER Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.9202 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22528 Z= 0.322 Angle : 0.524 10.509 30712 Z= 0.281 Chirality : 0.042 0.153 3916 Planarity : 0.003 0.052 3784 Dihedral : 4.456 38.775 3146 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 1.47 % Allowed : 11.74 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.97 (0.15), residues: 2970 helix: 2.27 (0.16), residues: 1034 sheet: 0.16 (0.19), residues: 660 loop : -0.41 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPGB 122 PHE 0.006 0.001 PHEEB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGDB 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 492 time to evaluate : 2.475 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8401 (t70) cc_final: 0.8106 (t0) REVERT: LA 55 GLU cc_start: 0.9306 (tp30) cc_final: 0.9024 (tp30) REVERT: LA 60 ASP cc_start: 0.8728 (t70) cc_final: 0.8088 (t0) REVERT: MA 55 GLU cc_start: 0.9275 (tp30) cc_final: 0.8806 (tp30) REVERT: MA 60 ASP cc_start: 0.8472 (t70) cc_final: 0.8067 (t0) REVERT: PA 60 ASP cc_start: 0.8504 (t70) cc_final: 0.8075 (t0) REVERT: QA 60 ASP cc_start: 0.8314 (t70) cc_final: 0.8068 (t0) REVERT: TA 37 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8994 (tttm) REVERT: EA 60 ASP cc_start: 0.8450 (t70) cc_final: 0.8083 (t0) REVERT: HB 124 ARG cc_start: 0.8956 (ttt-90) cc_final: 0.8724 (ttt-90) REVERT: PB 147 SER cc_start: 0.8124 (m) cc_final: 0.7679 (t) REVERT: TB 127 GLU cc_start: 0.8626 (mp0) cc_final: 0.8307 (mp0) outliers start: 35 outliers final: 26 residues processed: 506 average time/residue: 0.3116 time to fit residues: 247.6089 Evaluate side-chains 511 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 484 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain GA residue 73 ASN Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain QA residue 56 THR Chi-restraints excluded: chain QA residue 73 ASN Chi-restraints excluded: chain RA residue 45 SER Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 37 LYS Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain JB residue 123 THR Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain PB residue 99 GLU Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain SB residue 147 SER Chi-restraints excluded: chain TB residue 147 SER Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 0.0980 chunk 248 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 276 optimal weight: 6.9990 chunk 229 optimal weight: 0.0020 chunk 128 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- 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: 0.9173 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22528 Z= 0.170 Angle : 0.464 9.517 30712 Z= 0.250 Chirality : 0.039 0.162 3916 Planarity : 0.003 0.049 3784 Dihedral : 4.261 37.118 3146 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.27 % Rotamer: Outliers : 1.26 % Allowed : 12.37 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.98 (0.15), residues: 2970 helix: 2.18 (0.16), residues: 1056 sheet: 0.11 (0.19), residues: 660 loop : -0.32 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAB 122 PHE 0.003 0.000 PHEEB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.001 0.000 ARGQA 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 516 time to evaluate : 2.499 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8337 (t70) cc_final: 0.8032 (t0) REVERT: LA 55 GLU cc_start: 0.9309 (tp30) cc_final: 0.9051 (tp30) REVERT: LA 60 ASP cc_start: 0.8697 (t70) cc_final: 0.8072 (t0) REVERT: MA 55 GLU cc_start: 0.9287 (tp30) cc_final: 0.8802 (tp30) REVERT: MA 60 ASP cc_start: 0.8451 (t70) cc_final: 0.8035 (t0) REVERT: NA 55 GLU cc_start: 0.9256 (tp30) cc_final: 0.8748 (tp30) REVERT: OA 60 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8131 (t0) REVERT: PA 60 ASP cc_start: 0.8462 (t70) cc_final: 0.8060 (t0) REVERT: QA 55 GLU cc_start: 0.9139 (tp30) cc_final: 0.8768 (tp30) REVERT: QA 60 ASP cc_start: 0.8276 (t70) cc_final: 0.8013 (t0) REVERT: UA 68 GLU cc_start: 0.8555 (tp30) cc_final: 0.8331 (mm-30) REVERT: BA 55 GLU cc_start: 0.9132 (tp30) cc_final: 0.8891 (tp30) REVERT: HB 124 ARG cc_start: 0.8950 (ttt-90) cc_final: 0.8723 (ttt-90) REVERT: IB 109 ASN cc_start: 0.8913 (t0) cc_final: 0.8523 (t0) REVERT: TB 127 GLU cc_start: 0.8596 (mp0) cc_final: 0.8300 (mp0) outliers start: 30 outliers final: 23 residues processed: 534 average time/residue: 0.3321 time to fit residues: 281.8687 Evaluate side-chains 524 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 500 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 14 MET Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain OB residue 147 SER Chi-restraints excluded: chain PB residue 99 GLU Chi-restraints excluded: chain RB residue 123 THR Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.9181 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22528 Z= 0.212 Angle : 0.484 8.986 30712 Z= 0.261 Chirality : 0.040 0.176 3916 Planarity : 0.003 0.049 3784 Dihedral : 4.274 36.948 3146 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.64 % Allowed : 12.29 % Favored : 86.07 % 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: 0.95 (0.15), residues: 2970 helix: 2.16 (0.16), residues: 1056 sheet: 0.09 (0.19), residues: 660 loop : -0.34 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAB 122 PHE 0.004 0.001 PHEEB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.001 0.000 ARGDB 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 504 time to evaluate : 2.664 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8348 (t70) cc_final: 0.8042 (t0) REVERT: KA 62 LYS cc_start: 0.9524 (mtpp) cc_final: 0.9322 (mtpp) REVERT: LA 55 GLU cc_start: 0.9313 (tp30) cc_final: 0.9049 (tp30) REVERT: LA 60 ASP cc_start: 0.8703 (t70) cc_final: 0.8078 (t0) REVERT: MA 55 GLU cc_start: 0.9291 (tp30) cc_final: 0.8791 (tp30) REVERT: MA 60 ASP cc_start: 0.8471 (t70) cc_final: 0.8032 (t0) REVERT: NA 55 GLU cc_start: 0.9258 (tp30) cc_final: 0.8743 (tp30) REVERT: OA 60 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8154 (t0) REVERT: PA 60 ASP cc_start: 0.8465 (t70) cc_final: 0.8062 (t0) REVERT: QA 60 ASP cc_start: 0.8291 (t70) cc_final: 0.8016 (t0) REVERT: UA 68 GLU cc_start: 0.8568 (tp30) cc_final: 0.8353 (mm-30) REVERT: BA 55 GLU cc_start: 0.9133 (tp30) cc_final: 0.8882 (tp30) REVERT: IB 109 ASN cc_start: 0.8540 (t0) cc_final: 0.8179 (t0) REVERT: TB 127 GLU cc_start: 0.8606 (mp0) cc_final: 0.8308 (mp0) outliers start: 39 outliers final: 30 residues processed: 528 average time/residue: 0.3114 time to fit residues: 257.9334 Evaluate side-chains 530 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 499 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain GB residue 123 THR Chi-restraints excluded: chain IB residue 83 VAL Chi-restraints excluded: chain JB residue 83 VAL Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain PB residue 99 GLU Chi-restraints excluded: chain RB residue 123 THR Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain SB residue 123 THR Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain VB residue 83 VAL Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain CB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 175 optimal weight: 0.4980 chunk 187 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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: 0.9199 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22528 Z= 0.294 Angle : 0.520 8.906 30712 Z= 0.280 Chirality : 0.041 0.160 3916 Planarity : 0.003 0.051 3784 Dihedral : 4.450 37.434 3146 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.81 % Allowed : 12.21 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.89 (0.15), residues: 2970 helix: 2.23 (0.16), residues: 1034 sheet: 0.08 (0.19), residues: 660 loop : -0.46 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAB 122 PHE 0.005 0.001 PHESB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGHB 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 489 time to evaluate : 2.765 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8393 (t70) cc_final: 0.8084 (t0) REVERT: LA 55 GLU cc_start: 0.9300 (tp30) cc_final: 0.9024 (tp30) REVERT: LA 60 ASP cc_start: 0.8729 (t70) cc_final: 0.8084 (t0) REVERT: MA 55 GLU cc_start: 0.9294 (tp30) cc_final: 0.8806 (tp30) REVERT: MA 60 ASP cc_start: 0.8480 (t70) cc_final: 0.8037 (t0) REVERT: OA 60 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8159 (t0) REVERT: PA 60 ASP cc_start: 0.8479 (t70) cc_final: 0.8067 (t0) REVERT: QA 55 GLU cc_start: 0.9127 (tp30) cc_final: 0.8735 (tp30) REVERT: QA 60 ASP cc_start: 0.8328 (t70) cc_final: 0.8047 (t0) REVERT: TA 37 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9002 (tttm) REVERT: JB 99 GLU cc_start: 0.8919 (pt0) cc_final: 0.8684 (pm20) REVERT: TB 127 GLU cc_start: 0.8623 (mp0) cc_final: 0.8298 (mp0) outliers start: 43 outliers final: 38 residues processed: 514 average time/residue: 0.3213 time to fit residues: 259.9654 Evaluate side-chains 529 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 489 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 11 ILE Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain QA residue 56 THR Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 37 LYS Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain VA residue 49 SER Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain GB residue 123 THR Chi-restraints excluded: chain IB residue 83 VAL Chi-restraints excluded: chain JB residue 83 VAL Chi-restraints excluded: chain JB residue 110 SER Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain PB residue 99 GLU Chi-restraints excluded: chain PB residue 147 SER Chi-restraints excluded: chain QB residue 83 VAL Chi-restraints excluded: chain RB residue 123 THR Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain SB residue 123 THR Chi-restraints excluded: chain TB residue 147 SER Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain VB residue 83 VAL Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain CB residue 83 VAL Chi-restraints excluded: chain DB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 chunk 242 optimal weight: 0.4980 chunk 255 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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: 0.9195 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22528 Z= 0.266 Angle : 0.511 8.723 30712 Z= 0.276 Chirality : 0.041 0.163 3916 Planarity : 0.003 0.051 3784 Dihedral : 4.474 37.082 3146 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 1.98 % Allowed : 12.42 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.83 (0.15), residues: 2970 helix: 2.04 (0.16), residues: 1056 sheet: 0.06 (0.19), residues: 660 loop : -0.42 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAB 122 PHE 0.005 0.001 PHEEB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGHB 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 492 time to evaluate : 2.657 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8389 (t70) cc_final: 0.8081 (t0) REVERT: LA 55 GLU cc_start: 0.9298 (tp30) cc_final: 0.9022 (tp30) REVERT: LA 60 ASP cc_start: 0.8746 (t70) cc_final: 0.8095 (t0) REVERT: MA 55 GLU cc_start: 0.9285 (tp30) cc_final: 0.8800 (tp30) REVERT: MA 60 ASP cc_start: 0.8480 (t70) cc_final: 0.8037 (t0) REVERT: OA 60 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8199 (t0) REVERT: PA 60 ASP cc_start: 0.8478 (t70) cc_final: 0.8061 (t0) REVERT: QA 55 GLU cc_start: 0.9142 (tp30) cc_final: 0.8756 (tp30) REVERT: QA 60 ASP cc_start: 0.8289 (t70) cc_final: 0.8016 (t0) REVERT: IB 109 ASN cc_start: 0.8697 (t0) cc_final: 0.8320 (t0) REVERT: RB 127 GLU cc_start: 0.8356 (mp0) cc_final: 0.8087 (mp0) REVERT: TB 127 GLU cc_start: 0.8613 (mp0) cc_final: 0.8291 (mp0) outliers start: 47 outliers final: 41 residues processed: 520 average time/residue: 0.3125 time to fit residues: 255.5908 Evaluate side-chains 533 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 491 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain JA residue 69 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 11 ILE Chi-restraints excluded: chain NA residue 49 SER Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain QA residue 56 THR Chi-restraints excluded: chain QA residue 73 ASN Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 14 MET Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain VA residue 49 SER Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain GB residue 123 THR Chi-restraints excluded: chain IB residue 83 VAL Chi-restraints excluded: chain JB residue 83 VAL Chi-restraints excluded: chain JB residue 110 SER Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain PB residue 99 GLU Chi-restraints excluded: chain PB residue 147 SER Chi-restraints excluded: chain QB residue 83 VAL Chi-restraints excluded: chain RB residue 123 THR Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain SB residue 123 THR Chi-restraints excluded: chain TB residue 147 SER Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain VB residue 83 VAL Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain CB residue 83 VAL Chi-restraints excluded: chain DB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 10.0000 chunk 271 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 226 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 175 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.9156 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22528 Z= 0.142 Angle : 0.471 8.137 30712 Z= 0.253 Chirality : 0.038 0.203 3916 Planarity : 0.003 0.048 3784 Dihedral : 4.170 35.850 3146 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 1.52 % Allowed : 13.09 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.98 (0.15), residues: 2970 helix: 2.20 (0.16), residues: 1056 sheet: 0.10 (0.19), residues: 660 loop : -0.34 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPQB 122 PHE 0.003 0.000 PHEIB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGHB 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 541 time to evaluate : 2.609 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8331 (t70) cc_final: 0.8025 (t0) REVERT: HA 55 GLU cc_start: 0.9245 (tp30) cc_final: 0.8998 (tp30) REVERT: JA 51 LYS cc_start: 0.9226 (mttp) cc_final: 0.9020 (mtmm) REVERT: KA 68 GLU cc_start: 0.8570 (tp30) cc_final: 0.8354 (tp30) REVERT: LA 55 GLU cc_start: 0.9295 (tp30) cc_final: 0.9039 (tp30) REVERT: LA 60 ASP cc_start: 0.8711 (t70) cc_final: 0.8029 (t0) REVERT: MA 55 GLU cc_start: 0.9310 (tp30) cc_final: 0.8812 (tp30) REVERT: MA 60 ASP cc_start: 0.8448 (t70) cc_final: 0.8020 (t0) REVERT: NA 55 GLU cc_start: 0.9264 (tp30) cc_final: 0.8812 (tp30) REVERT: OA 60 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8203 (t0) REVERT: PA 60 ASP cc_start: 0.8424 (t70) cc_final: 0.8004 (t0) REVERT: QA 55 GLU cc_start: 0.9153 (tp30) cc_final: 0.8775 (tp30) REVERT: QA 60 ASP cc_start: 0.8274 (t70) cc_final: 0.7984 (t0) REVERT: BA 55 GLU cc_start: 0.9129 (tp30) cc_final: 0.8905 (tp30) REVERT: IB 109 ASN cc_start: 0.8578 (t0) cc_final: 0.8230 (t0) REVERT: JB 99 GLU cc_start: 0.8895 (pt0) cc_final: 0.8680 (pm20) REVERT: MB 127 GLU cc_start: 0.8473 (mp0) cc_final: 0.8255 (mp0) REVERT: RB 127 GLU cc_start: 0.8284 (mp0) cc_final: 0.8045 (mp0) REVERT: TB 127 GLU cc_start: 0.8579 (mp0) cc_final: 0.8282 (mp0) REVERT: BB 79 SER cc_start: 0.8468 (t) cc_final: 0.8154 (p) outliers start: 36 outliers final: 29 residues processed: 566 average time/residue: 0.3084 time to fit residues: 276.6844 Evaluate side-chains 551 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 521 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 11 ILE Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain IB residue 83 VAL Chi-restraints excluded: chain JB residue 83 VAL Chi-restraints excluded: chain JB residue 110 SER Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain PB residue 99 GLU Chi-restraints excluded: chain QB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain TB residue 147 SER Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain VB residue 83 VAL Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain CB residue 83 VAL Chi-restraints excluded: chain DB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.053141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.040609 restraints weight = 55053.263| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 2.32 r_work: 0.2276 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2148 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9316 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22528 Z= 0.192 Angle : 0.492 8.195 30712 Z= 0.264 Chirality : 0.039 0.158 3916 Planarity : 0.003 0.048 3784 Dihedral : 4.200 36.350 3146 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 1.39 % Allowed : 13.47 % Favored : 85.14 % 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: 0.95 (0.15), residues: 2970 helix: 2.18 (0.16), residues: 1056 sheet: 0.10 (0.19), residues: 660 loop : -0.37 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAB 122 PHE 0.003 0.001 PHEGB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGHB 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5735.34 seconds wall clock time: 102 minutes 46.72 seconds (6166.72 seconds total)