Starting phenix.real_space_refine on Sun Aug 4 11:16:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b63_44244/08_2024/9b63_44244.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b63_44244/08_2024/9b63_44244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b63_44244/08_2024/9b63_44244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b63_44244/08_2024/9b63_44244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b63_44244/08_2024/9b63_44244.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b63_44244/08_2024/9b63_44244.cif" } resolution = 2.76 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= 0.002 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 72 5.16 5 C 6909 2.51 5 N 1655 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "C TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10461 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1172 Chain: "A" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1161 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1168 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE B 623 " occ=0.44 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.56 residue: pdb=" N APHE D 623 " occ=0.40 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.60 Time building chain proxies: 7.57, per 1000 atoms: 0.72 Number of scatterers: 10461 At special positions: 0 Unit cell: (109.88, 111.52, 97.58, 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 72 16.00 O 1825 8.00 N 1655 7.00 C 6909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " 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: 4.34 Conformation dependent library (CDL) restraints added in 2.5 seconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 74.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.724A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 125 through 127 No H-bonds generated for 'chain 'H' and resid 125 through 127' Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.789A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 removed outlier: 3.536A pdb=" N PHE H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.644A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 126 removed outlier: 4.051A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.675A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 removed outlier: 3.515A pdb=" N ALA F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.675A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.915A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 removed outlier: 3.594A pdb=" N MET B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.784A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.594A pdb=" N TRP A 551 " --> pdb=" O PRO A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 788 through 825 removed outlier: 3.946A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.583A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 788 through 825 removed outlier: 3.697A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.715A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.509A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.926A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.826A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.828A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'E' and resid 78 through 79 removed outlier: 3.709A pdb=" N HIS E 60 " --> pdb=" O CYS E 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 79 842 hydrogen bonds defined for protein. 2456 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: 3.19 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3151 1.35 - 1.46: 3016 1.46 - 1.58: 4444 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 10723 Sorted by residual: bond pdb=" CG PRO B 512 " pdb=" CD PRO B 512 " ideal model delta sigma weight residual 1.503 1.377 0.126 3.40e-02 8.65e+02 1.38e+01 bond pdb=" CG1 ILE H 150 " pdb=" CD1 ILE H 150 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.46e-01 bond pdb=" CA PHE G 73 " pdb=" CB PHE G 73 " ideal model delta sigma weight residual 1.531 1.555 -0.024 3.28e-02 9.30e+02 5.30e-01 bond pdb=" N LYS F 41 " pdb=" CA LYS F 41 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.42e-02 4.96e+03 5.18e-01 bond pdb=" CA GLU F 70 " pdb=" CB GLU F 70 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.04e-01 ... (remaining 10718 not shown) Histogram of bond angle deviations from ideal: 90.39 - 99.32: 3 99.32 - 108.26: 288 108.26 - 117.19: 6947 117.19 - 126.13: 7116 126.13 - 135.06: 173 Bond angle restraints: 14527 Sorted by residual: angle pdb=" N PRO B 512 " pdb=" CD PRO B 512 " pdb=" CG PRO B 512 " ideal model delta sigma weight residual 103.20 90.39 12.81 1.50e+00 4.44e-01 7.30e+01 angle pdb=" CA PRO B 512 " pdb=" CB PRO B 512 " pdb=" CG PRO B 512 " ideal model delta sigma weight residual 104.50 92.66 11.84 1.90e+00 2.77e-01 3.88e+01 angle pdb=" CA PRO B 512 " pdb=" N PRO B 512 " pdb=" CD PRO B 512 " ideal model delta sigma weight residual 112.00 103.66 8.34 1.40e+00 5.10e-01 3.55e+01 angle pdb=" CB PRO B 512 " pdb=" CG PRO B 512 " pdb=" CD PRO B 512 " ideal model delta sigma weight residual 106.10 94.16 11.94 3.20e+00 9.77e-02 1.39e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" CB PRO B 512 " ideal model delta sigma weight residual 103.31 100.40 2.91 8.90e-01 1.26e+00 1.07e+01 ... (remaining 14522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5192 17.61 - 35.23: 658 35.23 - 52.84: 190 52.84 - 70.46: 37 70.46 - 88.07: 10 Dihedral angle restraints: 6087 sinusoidal: 2223 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 175.72 -82.72 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS G 67 " pdb=" SG CYS G 67 " pdb=" SG CYS G 77 " pdb=" CB CYS G 77 " ideal model delta sinusoidal sigma weight residual -86.00 -123.66 37.66 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" N PRO B 512 " pdb=" CG PRO B 512 " pdb=" CD PRO B 512 " pdb=" CB PRO B 512 " ideal model delta sinusoidal sigma weight residual -30.00 -72.35 42.35 1 1.50e+01 4.44e-03 1.11e+01 ... (remaining 6084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1046 0.025 - 0.051: 363 0.051 - 0.076: 170 0.076 - 0.101: 54 0.101 - 0.127: 13 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CA PHE E 107 " pdb=" N PHE E 107 " pdb=" C PHE E 107 " pdb=" CB PHE E 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA LYS H 41 " pdb=" N LYS H 41 " pdb=" C LYS H 41 " pdb=" CB LYS H 41 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PHE G 107 " pdb=" N PHE G 107 " pdb=" C PHE G 107 " pdb=" CB PHE G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 1643 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 511 " 0.022 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO B 512 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO G 108 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 60 " -0.007 2.00e-02 2.50e+03 8.59e-03 1.11e+00 pdb=" CG HIS H 60 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS H 60 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS H 60 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS H 60 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS H 60 " -0.002 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2063 2.77 - 3.30: 10166 3.30 - 3.84: 18583 3.84 - 4.37: 19973 4.37 - 4.90: 35422 Nonbonded interactions: 86207 Sorted by model distance: nonbonded pdb=" OG1 THR H 30 " pdb=" OG SER H 179 " model vdw 2.238 3.040 nonbonded pdb=" O GLU B 550 " pdb=" OG1 THR B 568 " model vdw 2.281 3.040 nonbonded pdb=" O PRO A 520 " pdb=" ND2 ASN A 619 " model vdw 2.292 3.120 nonbonded pdb=" O GLU D 550 " pdb=" OG1 THR D 568 " model vdw 2.302 3.040 nonbonded pdb=" NH2 ARG C 545 " pdb=" O ASN C 569 " model vdw 2.310 3.120 ... (remaining 86202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 511 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 626 or (resid 627 and (name N or name CA or name C or name O or name CB )) or \ resid 628 through 629 or (resid 784 and (name N or name CA or name C or name O o \ r name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 511 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 629 or (resid 784 and (name N or name CA or name C or name O or name CB )) or \ resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.810 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 0.126 10723 Z= 0.155 Angle : 0.474 12.813 14527 Z= 0.256 Chirality : 0.034 0.127 1646 Planarity : 0.003 0.031 1772 Dihedral : 17.288 88.074 3587 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.22 % Allowed : 25.12 % Favored : 72.67 % 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: 3.41 (0.23), residues: 1306 helix: 3.34 (0.16), residues: 948 sheet: -1.66 (1.87), residues: 10 loop : -0.90 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.011 0.001 HIS H 60 PHE 0.015 0.001 PHE G 97 TYR 0.010 0.001 TYR E 156 ARG 0.007 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7153 (tt) cc_final: 0.6741 (tm) outliers start: 24 outliers final: 25 residues processed: 156 average time/residue: 1.1564 time to fit residues: 196.4823 Evaluate side-chains 154 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10723 Z= 0.156 Angle : 0.449 7.465 14527 Z= 0.247 Chirality : 0.035 0.124 1646 Planarity : 0.003 0.033 1772 Dihedral : 5.645 58.623 1478 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.88 % Allowed : 22.25 % Favored : 73.87 % 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: 3.77 (0.23), residues: 1306 helix: 3.63 (0.15), residues: 952 sheet: -0.67 (1.77), residues: 10 loop : -0.94 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.008 0.001 HIS H 60 PHE 0.016 0.001 PHE D 584 TYR 0.010 0.001 TYR G 181 ARG 0.005 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7410 (m-10) cc_final: 0.7172 (m-10) REVERT: H 110 LEU cc_start: 0.7232 (tt) cc_final: 0.6827 (tm) REVERT: F 65 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.5993 (ppt-90) REVERT: C 594 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7282 (mtt-85) REVERT: E 21 PHE cc_start: 0.6888 (t80) cc_final: 0.6456 (t80) REVERT: E 185 LEU cc_start: 0.7279 (mt) cc_final: 0.6834 (mp) REVERT: G 55 GLU cc_start: 0.3142 (OUTLIER) cc_final: 0.2940 (tm-30) outliers start: 42 outliers final: 25 residues processed: 165 average time/residue: 0.9316 time to fit residues: 168.8512 Evaluate side-chains 161 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 96 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 115 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10723 Z= 0.138 Angle : 0.434 7.348 14527 Z= 0.235 Chirality : 0.035 0.150 1646 Planarity : 0.003 0.033 1772 Dihedral : 4.403 56.245 1449 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.42 % Allowed : 23.08 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.23), residues: 1306 helix: 3.79 (0.15), residues: 952 sheet: -0.08 (1.69), residues: 10 loop : -0.93 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.019 0.001 HIS E 60 PHE 0.013 0.001 PHE D 584 TYR 0.012 0.001 TYR B 523 ARG 0.005 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7262 (m-10) cc_final: 0.6981 (m-10) REVERT: H 110 LEU cc_start: 0.7095 (tt) cc_final: 0.6705 (tm) REVERT: H 200 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6893 (mtt) REVERT: F 65 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6016 (ppt-90) REVERT: C 594 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7283 (mtt-85) REVERT: B 511 LYS cc_start: 0.6149 (tmtm) cc_final: 0.5935 (mttt) REVERT: B 570 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: G 55 GLU cc_start: 0.3079 (OUTLIER) cc_final: 0.2820 (tm-30) outliers start: 37 outliers final: 20 residues processed: 158 average time/residue: 0.9806 time to fit residues: 169.6956 Evaluate side-chains 157 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 116 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10723 Z= 0.223 Angle : 0.476 5.046 14527 Z= 0.264 Chirality : 0.037 0.144 1646 Planarity : 0.003 0.035 1772 Dihedral : 4.074 56.303 1443 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.16 % Allowed : 21.98 % Favored : 73.87 % 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: 3.58 (0.23), residues: 1306 helix: 3.47 (0.16), residues: 948 sheet: 0.01 (0.88), residues: 40 loop : -1.01 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 578 HIS 0.004 0.001 HIS G 205 PHE 0.018 0.002 PHE C 584 TYR 0.010 0.001 TYR C 616 ARG 0.005 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7337 (tt) cc_final: 0.6978 (tm) REVERT: H 200 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7118 (mtt) REVERT: C 594 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7388 (mtt-85) REVERT: C 623 PHE cc_start: 0.8117 (m-10) cc_final: 0.7899 (m-10) REVERT: B 570 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6677 (mt-10) REVERT: E 21 PHE cc_start: 0.6921 (t80) cc_final: 0.6476 (t80) REVERT: G 55 GLU cc_start: 0.3096 (OUTLIER) cc_final: 0.2794 (tm-30) outliers start: 45 outliers final: 28 residues processed: 162 average time/residue: 0.9162 time to fit residues: 163.6381 Evaluate side-chains 162 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10723 Z= 0.169 Angle : 0.452 7.943 14527 Z= 0.247 Chirality : 0.036 0.140 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.987 57.197 1443 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.34 % Allowed : 22.16 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.23), residues: 1306 helix: 3.56 (0.16), residues: 948 sheet: 0.46 (1.67), residues: 10 loop : -0.97 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.014 0.001 PHE D 584 TYR 0.013 0.001 TYR B 523 ARG 0.003 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7214 (tt) cc_final: 0.6865 (tm) REVERT: H 200 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7058 (mtt) REVERT: F 10 MET cc_start: 0.7490 (tpp) cc_final: 0.6735 (tpt) REVERT: F 65 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6021 (ppt-90) REVERT: C 594 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7345 (mtt-85) REVERT: B 570 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6666 (mt-10) REVERT: E 21 PHE cc_start: 0.6996 (t80) cc_final: 0.6539 (t80) REVERT: E 24 MET cc_start: 0.5371 (tpt) cc_final: 0.5159 (tpt) REVERT: G 55 GLU cc_start: 0.3095 (OUTLIER) cc_final: 0.2781 (tm-30) outliers start: 47 outliers final: 30 residues processed: 164 average time/residue: 0.8641 time to fit residues: 156.6230 Evaluate side-chains 167 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10723 Z= 0.146 Angle : 0.427 6.728 14527 Z= 0.236 Chirality : 0.035 0.136 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.888 56.979 1443 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.51 % Allowed : 23.36 % Favored : 73.13 % 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: 3.85 (0.23), residues: 1306 helix: 3.69 (0.16), residues: 948 sheet: 1.07 (1.79), residues: 10 loop : -0.96 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.002 0.001 HIS F 205 PHE 0.012 0.001 PHE D 584 TYR 0.014 0.001 TYR B 523 ARG 0.002 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7138 (tt) cc_final: 0.6790 (tm) REVERT: H 122 ILE cc_start: 0.7318 (mm) cc_final: 0.6791 (mm) REVERT: H 200 MET cc_start: 0.7542 (mmm) cc_final: 0.7085 (mtt) REVERT: F 10 MET cc_start: 0.7449 (tpp) cc_final: 0.6642 (tpt) REVERT: F 65 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.6019 (ppt-90) REVERT: C 594 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7315 (mtt-85) REVERT: B 570 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: G 55 GLU cc_start: 0.3055 (OUTLIER) cc_final: 0.2725 (tm-30) outliers start: 38 outliers final: 27 residues processed: 159 average time/residue: 0.9747 time to fit residues: 170.4435 Evaluate side-chains 162 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 0.0060 chunk 76 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10723 Z= 0.133 Angle : 0.423 7.236 14527 Z= 0.231 Chirality : 0.035 0.135 1646 Planarity : 0.003 0.034 1772 Dihedral : 3.813 56.857 1443 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.88 % Allowed : 23.08 % Favored : 73.04 % 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: 3.98 (0.23), residues: 1306 helix: 3.80 (0.16), residues: 948 sheet: 1.34 (1.94), residues: 10 loop : -0.96 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.002 0.001 HIS F 205 PHE 0.012 0.001 PHE D 584 TYR 0.014 0.001 TYR B 523 ARG 0.002 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7038 (tt) cc_final: 0.6649 (tm) REVERT: H 122 ILE cc_start: 0.7313 (mm) cc_final: 0.6795 (mm) REVERT: H 200 MET cc_start: 0.7653 (mmm) cc_final: 0.7218 (mtt) REVERT: F 10 MET cc_start: 0.7465 (tpp) cc_final: 0.6669 (tpt) REVERT: F 65 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6000 (ppt-90) REVERT: C 594 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7284 (mtt-85) REVERT: B 527 MET cc_start: 0.7758 (ttp) cc_final: 0.7550 (ptm) REVERT: B 570 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: A 629 MET cc_start: 0.7817 (ptm) cc_final: 0.7523 (ptp) REVERT: D 629 MET cc_start: 0.6314 (tpt) cc_final: 0.5919 (mmt) REVERT: E 24 MET cc_start: 0.5063 (tpt) cc_final: 0.4842 (tpt) REVERT: G 55 GLU cc_start: 0.3045 (OUTLIER) cc_final: 0.2707 (tm-30) outliers start: 42 outliers final: 29 residues processed: 163 average time/residue: 0.9810 time to fit residues: 176.2434 Evaluate side-chains 164 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10723 Z= 0.150 Angle : 0.435 8.014 14527 Z= 0.237 Chirality : 0.035 0.133 1646 Planarity : 0.003 0.034 1772 Dihedral : 3.810 56.561 1441 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.60 % Allowed : 23.64 % Favored : 72.76 % 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: 3.90 (0.23), residues: 1306 helix: 3.74 (0.16), residues: 948 sheet: 1.08 (1.84), residues: 10 loop : -0.97 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.003 0.001 HIS F 205 PHE 0.012 0.001 PHE D 584 TYR 0.014 0.001 TYR B 523 ARG 0.004 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7043 (tt) cc_final: 0.6666 (tm) REVERT: H 122 ILE cc_start: 0.7318 (mm) cc_final: 0.6801 (mm) REVERT: H 200 MET cc_start: 0.7666 (mmm) cc_final: 0.7250 (mtt) REVERT: F 10 MET cc_start: 0.7478 (tpp) cc_final: 0.6991 (tpt) REVERT: F 65 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6041 (ppt-90) REVERT: C 594 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7321 (mtt-85) REVERT: B 570 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6616 (mt-10) REVERT: D 629 MET cc_start: 0.6363 (tpt) cc_final: 0.5947 (mmt) REVERT: E 117 MET cc_start: 0.4356 (tpt) cc_final: 0.4151 (tpt) REVERT: E 208 LEU cc_start: 0.4431 (OUTLIER) cc_final: 0.3730 (pp) REVERT: G 55 GLU cc_start: 0.2987 (OUTLIER) cc_final: 0.2652 (tm-30) outliers start: 39 outliers final: 30 residues processed: 159 average time/residue: 0.9517 time to fit residues: 166.2344 Evaluate side-chains 164 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 103 optimal weight: 0.0030 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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: 0.7513 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10723 Z= 0.136 Angle : 0.434 7.854 14527 Z= 0.234 Chirality : 0.035 0.130 1646 Planarity : 0.003 0.034 1772 Dihedral : 3.764 56.145 1441 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.69 % Allowed : 23.55 % Favored : 72.76 % 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: 3.99 (0.23), residues: 1306 helix: 3.82 (0.16), residues: 948 sheet: 1.05 (1.81), residues: 10 loop : -0.97 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.012 0.001 PHE D 584 TYR 0.015 0.001 TYR B 523 ARG 0.006 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7003 (tt) cc_final: 0.6620 (tm) REVERT: H 122 ILE cc_start: 0.7361 (mm) cc_final: 0.6847 (mm) REVERT: H 200 MET cc_start: 0.7670 (mmm) cc_final: 0.7234 (mtt) REVERT: F 10 MET cc_start: 0.7484 (tpp) cc_final: 0.6843 (tpt) REVERT: F 65 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6018 (ppt-90) REVERT: C 594 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7294 (mtt-85) REVERT: B 570 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: D 629 MET cc_start: 0.6367 (tpt) cc_final: 0.5949 (mmt) REVERT: E 208 LEU cc_start: 0.4472 (OUTLIER) cc_final: 0.3795 (pp) REVERT: G 55 GLU cc_start: 0.2971 (OUTLIER) cc_final: 0.2643 (tm-30) outliers start: 40 outliers final: 31 residues processed: 155 average time/residue: 0.9132 time to fit residues: 155.6618 Evaluate side-chains 164 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7525 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10723 Z= 0.148 Angle : 0.442 8.129 14527 Z= 0.239 Chirality : 0.035 0.131 1646 Planarity : 0.003 0.034 1772 Dihedral : 3.797 55.874 1441 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.23 % Allowed : 23.82 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.23), residues: 1306 helix: 3.76 (0.16), residues: 948 sheet: 0.98 (1.83), residues: 10 loop : -0.97 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.012 0.001 PHE H 142 TYR 0.015 0.001 TYR B 523 ARG 0.007 0.000 ARG C 545 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7035 (tt) cc_final: 0.6650 (tm) REVERT: H 122 ILE cc_start: 0.7360 (mm) cc_final: 0.6840 (mm) REVERT: H 200 MET cc_start: 0.7679 (mmm) cc_final: 0.7257 (mtt) REVERT: F 65 ARG cc_start: 0.6497 (OUTLIER) cc_final: 0.6036 (ppt-90) REVERT: C 594 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7307 (mtt-85) REVERT: B 570 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: D 629 MET cc_start: 0.6378 (tpt) cc_final: 0.5952 (mmt) REVERT: E 208 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.3809 (pp) REVERT: G 55 GLU cc_start: 0.2987 (OUTLIER) cc_final: 0.2649 (tm-30) outliers start: 35 outliers final: 29 residues processed: 150 average time/residue: 0.9628 time to fit residues: 158.5627 Evaluate side-chains 161 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.245964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.187799 restraints weight = 27338.853| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 3.87 r_work: 0.3653 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10723 Z= 0.158 Angle : 0.454 8.824 14527 Z= 0.243 Chirality : 0.035 0.130 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.842 55.352 1441 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.23 % Allowed : 24.01 % Favored : 72.76 % 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: 3.85 (0.23), residues: 1306 helix: 3.70 (0.15), residues: 948 sheet: 1.22 (1.83), residues: 10 loop : -0.97 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.013 0.001 PHE D 584 TYR 0.015 0.001 TYR B 523 ARG 0.006 0.000 ARG C 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3570.14 seconds wall clock time: 63 minutes 19.77 seconds (3799.77 seconds total)