Starting phenix.real_space_refine on Fri Feb 16 18:56:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/02_2024/6xmx_22265_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/02_2024/6xmx_22265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/02_2024/6xmx_22265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/02_2024/6xmx_22265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/02_2024/6xmx_22265_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/02_2024/6xmx_22265_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians S 88 5.16 5 Cl 8 4.86 5 C 5136 2.51 5 N 1408 2.21 5 O 1432 1.98 5 H 7942 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16014 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "B" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "C" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "G" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "H" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.17, per 1000 atoms: 0.45 Number of scatterers: 16014 At special positions: 0 Unit cell: (137.775, 77.55, 113.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 88 16.00 O 1432 8.00 N 1408 7.00 C 5136 6.00 H 7942 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.59 Conformation dependent library (CDL) restraints added in 1.6 seconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 8 sheets defined 54.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'B' and resid 14 through 27 Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 55 through 62 Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'C' and resid 14 through 27 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 55 through 62 Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'E' and resid 14 through 27 Processing helix chain 'E' and resid 47 through 53 Processing helix chain 'E' and resid 55 through 62 Processing helix chain 'E' and resid 80 through 92 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 115 through 127 Processing helix chain 'F' and resid 14 through 27 Processing helix chain 'F' and resid 47 through 53 Processing helix chain 'F' and resid 55 through 62 Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 115 through 127 Processing helix chain 'G' and resid 14 through 27 Processing helix chain 'G' and resid 47 through 53 Processing helix chain 'G' and resid 55 through 62 Processing helix chain 'G' and resid 80 through 92 Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 115 through 127 Processing helix chain 'H' and resid 14 through 27 Processing helix chain 'H' and resid 47 through 53 Processing helix chain 'H' and resid 55 through 62 Processing helix chain 'H' and resid 80 through 92 Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 115 through 127 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 45 Processing sheet with id= B, first strand: chain 'B' and resid 41 through 45 Processing sheet with id= C, first strand: chain 'C' and resid 41 through 45 Processing sheet with id= D, first strand: chain 'D' and resid 41 through 45 Processing sheet with id= E, first strand: chain 'E' and resid 41 through 45 Processing sheet with id= F, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= G, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= H, first strand: chain 'H' and resid 41 through 45 400 hydrogen bonds defined for protein. 1152 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: 5.06 Time building geometry restraints manager: 13.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7903 1.02 - 1.21: 39 1.21 - 1.41: 3312 1.41 - 1.61: 4752 1.61 - 1.80: 144 Bond restraints: 16150 Sorted by residual: bond pdb=" C24 U52 A 401 " pdb=" N20 U52 A 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 D 401 " pdb=" N20 U52 D 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 G 401 " pdb=" N20 U52 G 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 C 401 " pdb=" N20 U52 C 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C24 U52 B 401 " pdb=" N20 U52 B 401 " ideal model delta sigma weight residual 1.352 1.424 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 16145 not shown) Histogram of bond angle deviations from ideal: 76.18 - 88.57: 4 88.57 - 100.96: 39 100.96 - 113.35: 19271 113.35 - 125.74: 9554 125.74 - 138.13: 146 Bond angle restraints: 29014 Sorted by residual: angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB2 GLU A 81 " ideal model delta sigma weight residual 109.00 76.18 32.82 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 109.00 77.25 31.75 3.00e+00 1.11e-01 1.12e+02 angle pdb=" HB2 GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 110.00 138.13 -28.13 3.00e+00 1.11e-01 8.79e+01 angle pdb=" CG GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB2 GLU A 81 " ideal model delta sigma weight residual 108.00 81.68 26.32 3.00e+00 1.11e-01 7.70e+01 angle pdb=" CG GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 108.00 83.18 24.82 3.00e+00 1.11e-01 6.85e+01 ... (remaining 29009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6763 16.69 - 33.38: 562 33.38 - 50.07: 185 50.07 - 66.76: 78 66.76 - 83.45: 18 Dihedral angle restraints: 7606 sinusoidal: 4286 harmonic: 3320 Sorted by residual: dihedral pdb=" N GLU H 81 " pdb=" CA GLU H 81 " pdb=" CB GLU H 81 " pdb=" CG GLU H 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.59 50.41 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" N GLU D 81 " pdb=" CA GLU D 81 " pdb=" CB GLU D 81 " pdb=" CG GLU D 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.61 50.39 3 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" N GLU B 81 " pdb=" CA GLU B 81 " pdb=" CB GLU B 81 " pdb=" CG GLU B 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.61 50.39 3 1.50e+01 4.44e-03 8.89e+00 ... (remaining 7603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 683 0.034 - 0.067: 325 0.067 - 0.100: 172 0.100 - 0.134: 84 0.134 - 0.167: 32 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CB VAL C 117 " pdb=" CA VAL C 117 " pdb=" CG1 VAL C 117 " pdb=" CG2 VAL C 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CB VAL E 117 " pdb=" CA VAL E 117 " pdb=" CG1 VAL E 117 " pdb=" CG2 VAL E 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PRO E 80 " pdb=" N PRO E 80 " pdb=" C PRO E 80 " pdb=" CB PRO E 80 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1293 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 43 " 0.015 2.00e-02 2.50e+03 1.41e-02 6.00e+00 pdb=" CG PHE B 43 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 43 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 43 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE B 43 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE B 43 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 43 " -0.014 2.00e-02 2.50e+03 1.39e-02 5.81e+00 pdb=" CG PHE E 43 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 43 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE E 43 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 43 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 43 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 43 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE E 43 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE E 43 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE E 43 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE E 43 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE E 43 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 43 " 0.016 2.00e-02 2.50e+03 1.37e-02 5.60e+00 pdb=" CG PHE D 43 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE D 43 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE D 43 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 43 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 43 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE D 43 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE D 43 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE D 43 " -0.002 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 204 2.04 - 2.68: 25633 2.68 - 3.32: 46747 3.32 - 3.96: 59762 3.96 - 4.60: 95076 Nonbonded interactions: 227422 Sorted by model distance: nonbonded pdb=" O TYR A 58 " pdb=" HG1 THR A 62 " model vdw 1.397 1.850 nonbonded pdb=" O TYR B 58 " pdb=" HG1 THR B 62 " model vdw 1.483 1.850 nonbonded pdb=" O TYR C 58 " pdb=" HG1 THR C 62 " model vdw 1.504 1.850 nonbonded pdb=" O TYR G 58 " pdb=" HG1 THR G 62 " model vdw 1.534 1.850 nonbonded pdb=" O THR G 92 " pdb=" HG SER G 93 " model vdw 1.539 1.850 ... (remaining 227417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 128 or resid 401)) selection = (chain 'B' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'C' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'D' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'E' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'F' and (resid 7 through 107 or (resid 108 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) \ selection = (chain 'G' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'H' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.250 Extract box with map and model: 4.380 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 51.050 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5250 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 : 0.012 0.083 8208 Z= 0.763 Angle : 1.120 9.615 11096 Z= 0.621 Chirality : 0.057 0.167 1296 Planarity : 0.006 0.023 1368 Dihedral : 15.974 83.454 3168 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.89 % Allowed : 5.36 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 960 helix: -1.09 (0.16), residues: 584 sheet: None (None), residues: 0 loop : -0.24 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.005 HIS G 46 PHE 0.040 0.005 PHE B 43 TYR 0.016 0.004 TYR E 111 ARG 0.025 0.003 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 299 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ILE cc_start: 0.6262 (mt) cc_final: 0.5823 (mt) REVERT: D 105 VAL cc_start: 0.6412 (t) cc_final: 0.6160 (t) REVERT: F 30 ILE cc_start: 0.5867 (mt) cc_final: 0.5556 (mt) outliers start: 8 outliers final: 2 residues processed: 304 average time/residue: 0.4431 time to fit residues: 180.4485 Evaluate side-chains 166 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5514 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8208 Z= 0.164 Angle : 0.518 9.125 11096 Z= 0.278 Chirality : 0.041 0.154 1296 Planarity : 0.003 0.024 1368 Dihedral : 6.207 57.748 1286 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.45 % Allowed : 15.62 % Favored : 82.92 % 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: 1.49 (0.26), residues: 960 helix: 1.50 (0.21), residues: 584 sheet: None (None), residues: 0 loop : 0.33 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 46 PHE 0.020 0.001 PHE H 124 TYR 0.017 0.002 TYR E 58 ARG 0.007 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.6192 (t0) cc_final: 0.5908 (t0) REVERT: C 86 LEU cc_start: 0.7019 (mt) cc_final: 0.6816 (mt) REVERT: D 30 ILE cc_start: 0.6236 (mt) cc_final: 0.5927 (mt) outliers start: 13 outliers final: 6 residues processed: 191 average time/residue: 0.4038 time to fit residues: 107.3953 Evaluate side-chains 163 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN D 42 GLN F 96 ASN G 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8208 Z= 0.299 Angle : 0.661 8.003 11096 Z= 0.352 Chirality : 0.045 0.181 1296 Planarity : 0.005 0.060 1368 Dihedral : 8.165 69.979 1280 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.46 % Allowed : 15.96 % Favored : 81.58 % 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: 0.67 (0.27), residues: 960 helix: 0.95 (0.21), residues: 592 sheet: -1.26 (0.39), residues: 80 loop : 0.17 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 14 PHE 0.015 0.002 PHE B 43 TYR 0.023 0.003 TYR B 58 ARG 0.006 0.001 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5402 (tt0) REVERT: H 22 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4880 (tt) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.3767 time to fit residues: 98.4532 Evaluate side-chains 174 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8208 Z= 0.140 Angle : 0.489 9.161 11096 Z= 0.260 Chirality : 0.041 0.146 1296 Planarity : 0.003 0.032 1368 Dihedral : 6.779 58.233 1280 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.90 % Allowed : 17.41 % Favored : 80.69 % 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: 1.48 (0.27), residues: 960 helix: 1.56 (0.21), residues: 592 sheet: None (None), residues: 0 loop : 0.14 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 46 PHE 0.010 0.001 PHE C 83 TYR 0.026 0.002 TYR E 58 ARG 0.004 0.000 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4812 (tt) REVERT: H 26 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6739 (ttt90) outliers start: 17 outliers final: 11 residues processed: 173 average time/residue: 0.4007 time to fit residues: 95.9483 Evaluate side-chains 165 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 26 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8208 Z= 0.176 Angle : 0.509 8.460 11096 Z= 0.270 Chirality : 0.041 0.152 1296 Planarity : 0.003 0.034 1368 Dihedral : 7.166 61.847 1280 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.57 % Allowed : 15.85 % Favored : 80.58 % 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: 1.55 (0.27), residues: 960 helix: 1.67 (0.21), residues: 592 sheet: -0.82 (0.42), residues: 80 loop : 0.42 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 14 PHE 0.007 0.001 PHE C 83 TYR 0.018 0.002 TYR E 58 ARG 0.002 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 MET cc_start: 0.6928 (mmt) cc_final: 0.6265 (mpp) REVERT: E 101 ASN cc_start: 0.3152 (OUTLIER) cc_final: 0.2900 (p0) REVERT: F 25 LEU cc_start: 0.7862 (mt) cc_final: 0.7474 (mt) REVERT: H 22 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4879 (tt) outliers start: 32 outliers final: 19 residues processed: 186 average time/residue: 0.3746 time to fit residues: 97.8879 Evaluate side-chains 182 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8208 Z= 0.217 Angle : 0.559 10.972 11096 Z= 0.298 Chirality : 0.042 0.159 1296 Planarity : 0.004 0.037 1368 Dihedral : 7.422 64.402 1280 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.35 % Allowed : 17.52 % Favored : 79.13 % 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: 1.38 (0.27), residues: 960 helix: 1.62 (0.21), residues: 576 sheet: -0.74 (0.46), residues: 80 loop : 0.19 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 116 PHE 0.011 0.001 PHE B 124 TYR 0.020 0.002 TYR E 58 ARG 0.003 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.6428 (mtm110) cc_final: 0.6218 (mtm110) REVERT: D 103 MET cc_start: 0.6919 (mmt) cc_final: 0.6446 (mpp) REVERT: F 25 LEU cc_start: 0.7825 (mt) cc_final: 0.7413 (mt) REVERT: F 103 MET cc_start: 0.7277 (mmm) cc_final: 0.7005 (mmp) REVERT: G 106 MET cc_start: 0.7217 (tpt) cc_final: 0.6778 (tpt) REVERT: H 22 LEU cc_start: 0.5312 (OUTLIER) cc_final: 0.4921 (tt) outliers start: 30 outliers final: 24 residues processed: 187 average time/residue: 0.4338 time to fit residues: 110.4155 Evaluate side-chains 183 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8208 Z= 0.144 Angle : 0.488 10.623 11096 Z= 0.258 Chirality : 0.040 0.141 1296 Planarity : 0.003 0.036 1368 Dihedral : 6.798 58.982 1280 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.01 % Allowed : 18.75 % Favored : 79.24 % 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: 1.89 (0.27), residues: 960 helix: 2.07 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.05 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 46 PHE 0.012 0.001 PHE B 124 TYR 0.028 0.002 TYR A 58 ARG 0.004 0.000 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 MET cc_start: 0.6916 (mmt) cc_final: 0.6394 (mpp) REVERT: E 101 ASN cc_start: 0.2980 (OUTLIER) cc_final: 0.2716 (p0) REVERT: F 25 LEU cc_start: 0.7869 (mt) cc_final: 0.7503 (mt) REVERT: G 106 MET cc_start: 0.7198 (tpt) cc_final: 0.6722 (tpt) REVERT: H 22 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4852 (tt) outliers start: 18 outliers final: 13 residues processed: 170 average time/residue: 0.4179 time to fit residues: 97.5437 Evaluate side-chains 167 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.5990 moved from start: 0.7713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8208 Z= 0.163 Angle : 0.511 9.670 11096 Z= 0.268 Chirality : 0.041 0.147 1296 Planarity : 0.003 0.041 1368 Dihedral : 6.820 55.933 1280 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.34 % Allowed : 18.97 % Favored : 78.68 % 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: 1.91 (0.27), residues: 960 helix: 2.10 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.04 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 14 PHE 0.010 0.001 PHE C 83 TYR 0.038 0.002 TYR A 58 ARG 0.006 0.000 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 MET cc_start: 0.6966 (mmt) cc_final: 0.6421 (mpp) REVERT: F 25 LEU cc_start: 0.7864 (mt) cc_final: 0.7477 (mt) REVERT: F 103 MET cc_start: 0.6971 (mmp) cc_final: 0.6701 (mmm) REVERT: G 106 MET cc_start: 0.7229 (tpt) cc_final: 0.6742 (tpt) REVERT: H 22 LEU cc_start: 0.5256 (OUTLIER) cc_final: 0.4894 (tt) outliers start: 21 outliers final: 19 residues processed: 172 average time/residue: 0.4234 time to fit residues: 100.8829 Evaluate side-chains 174 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0870 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.7857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8208 Z= 0.154 Angle : 0.506 9.570 11096 Z= 0.264 Chirality : 0.041 0.142 1296 Planarity : 0.003 0.051 1368 Dihedral : 6.747 56.432 1280 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.46 % Allowed : 18.97 % Favored : 78.57 % 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: 2.03 (0.27), residues: 960 helix: 2.21 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.05 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 14 PHE 0.008 0.001 PHE G 83 TYR 0.042 0.002 TYR A 58 ARG 0.006 0.000 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 MET cc_start: 0.6939 (mmt) cc_final: 0.6411 (mpp) REVERT: F 25 LEU cc_start: 0.7888 (mt) cc_final: 0.7528 (mt) REVERT: G 106 MET cc_start: 0.7243 (tpt) cc_final: 0.6755 (tpt) REVERT: H 22 LEU cc_start: 0.5231 (OUTLIER) cc_final: 0.4861 (tt) outliers start: 22 outliers final: 18 residues processed: 172 average time/residue: 0.4031 time to fit residues: 95.5615 Evaluate side-chains 175 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.8171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8208 Z= 0.247 Angle : 0.594 9.196 11096 Z= 0.315 Chirality : 0.043 0.166 1296 Planarity : 0.004 0.052 1368 Dihedral : 7.538 61.995 1280 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.46 % Allowed : 18.86 % Favored : 78.68 % 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: 1.29 (0.27), residues: 960 helix: 1.56 (0.21), residues: 576 sheet: -0.94 (0.49), residues: 80 loop : 0.19 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 14 PHE 0.010 0.002 PHE C 83 TYR 0.032 0.003 TYR A 58 ARG 0.005 0.001 ARG H 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 MET cc_start: 0.7050 (mmt) cc_final: 0.6512 (mpp) REVERT: F 25 LEU cc_start: 0.7938 (mt) cc_final: 0.7536 (mt) REVERT: H 22 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.5215 (mt) REVERT: H 90 MET cc_start: 0.6932 (mtp) cc_final: 0.6664 (mtp) outliers start: 22 outliers final: 19 residues processed: 172 average time/residue: 0.4512 time to fit residues: 105.7410 Evaluate side-chains 175 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.183301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.156747 restraints weight = 27225.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.163731 restraints weight = 10835.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.167970 restraints weight = 5574.973| |-----------------------------------------------------------------------------| r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.8295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8208 Z= 0.167 Angle : 0.523 9.487 11096 Z= 0.273 Chirality : 0.041 0.144 1296 Planarity : 0.003 0.048 1368 Dihedral : 7.073 61.143 1280 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.12 % Allowed : 19.31 % Favored : 78.57 % 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: 1.63 (0.27), residues: 960 helix: 1.86 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.05 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 46 PHE 0.010 0.001 PHE C 61 TYR 0.030 0.002 TYR A 58 ARG 0.007 0.000 ARG D 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4003.79 seconds wall clock time: 71 minutes 40.84 seconds (4300.84 seconds total)