Starting phenix.real_space_refine on Thu Nov 16 18:01:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/11_2023/6xmx_22265_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/11_2023/6xmx_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_22265/11_2023/6xmx_22265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/11_2023/6xmx_22265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/11_2023/6xmx_22265_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/11_2023/6xmx_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-1.21rc1-5144/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: 7.62, per 1000 atoms: 0.48 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: 13.17 Conformation dependent library (CDL) restraints added in 1.7 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: 2.75 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: 5.73 Time building geometry restraints manager: 13.56 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: 5731 16.69 - 33.38: 538 33.38 - 50.07: 153 50.07 - 66.76: 54 66.76 - 83.45: 18 Dihedral angle restraints: 6494 sinusoidal: 3174 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 6491 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 4.240 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 54.740 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.510 ------------------------------------------------------------------------------- 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 : 16.356 83.454 3008 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 *********************** 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 : 1.209 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 outliers start: 8 outliers final: 2 residues processed: 304 average time/residue: 0.4374 time to fit residues: 178.0554 Evaluate side-chains 166 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.408 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2436 time to fit residues: 2.5380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.5489 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8208 Z= 0.152 Angle : 0.514 9.320 11096 Z= 0.275 Chirality : 0.041 0.153 1296 Planarity : 0.003 0.026 1368 Dihedral : 6.055 43.266 1120 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.56 % Allowed : 15.62 % Favored : 82.81 % 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 (0.26), residues: 960 helix: 1.48 (0.21), residues: 584 sheet: None (None), residues: 0 loop : 0.33 (0.32), residues: 376 *********************** 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 198 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.193 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 outliers start: 14 outliers final: 7 residues processed: 192 average time/residue: 0.3907 time to fit residues: 104.2417 Evaluate side-chains 162 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1746 time to fit residues: 3.6623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN G 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8208 Z= 0.249 Angle : 0.597 8.243 11096 Z= 0.317 Chirality : 0.043 0.172 1296 Planarity : 0.004 0.049 1368 Dihedral : 7.774 59.860 1120 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.90 % Allowed : 16.52 % 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: 1.16 (0.27), residues: 960 helix: 1.40 (0.21), residues: 592 sheet: -1.27 (0.38), residues: 80 loop : 0.28 (0.39), residues: 288 *********************** 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 183 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.498 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 outliers start: 17 outliers final: 15 residues processed: 174 average time/residue: 0.3879 time to fit residues: 95.2187 Evaluate side-chains 170 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1808 time to fit residues: 6.5942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.5775 moved from start: 0.5850 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= 0.135 Angle : 0.474 9.798 11096 Z= 0.250 Chirality : 0.040 0.143 1296 Planarity : 0.002 0.025 1368 Dihedral : 6.738 51.791 1120 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.12 % Allowed : 16.07 % Favored : 82.81 % 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: 1.87 (0.27), residues: 960 helix: 1.90 (0.22), residues: 592 sheet: None (None), residues: 0 loop : 0.25 (0.32), residues: 368 *********************** 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 176 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.316 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 outliers start: 10 outliers final: 6 residues processed: 174 average time/residue: 0.3936 time to fit residues: 95.9618 Evaluate side-chains 154 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1774 time to fit residues: 3.6089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8208 Z= 0.260 Angle : 0.608 8.672 11096 Z= 0.325 Chirality : 0.043 0.171 1296 Planarity : 0.004 0.053 1368 Dihedral : 8.266 63.442 1120 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.79 % Allowed : 16.74 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 960 helix: 1.40 (0.21), residues: 576 sheet: -0.87 (0.45), residues: 80 loop : 0.05 (0.36), residues: 304 *********************** 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 187 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.392 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 outliers start: 16 outliers final: 11 residues processed: 176 average time/residue: 0.4321 time to fit residues: 103.2918 Evaluate side-chains 167 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1829 time to fit residues: 5.3180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.6013 moved from start: 0.7285 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= 0.187 Angle : 0.520 8.371 11096 Z= 0.278 Chirality : 0.041 0.150 1296 Planarity : 0.003 0.033 1368 Dihedral : 7.634 60.351 1120 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.33 % Allowed : 18.19 % Favored : 81.47 % 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: 1.36 (0.26), residues: 960 helix: 1.62 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.11 (0.30), residues: 384 *********************** 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 166 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.324 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 outliers start: 3 outliers final: 3 residues processed: 165 average time/residue: 0.4371 time to fit residues: 100.2688 Evaluate side-chains 156 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2352 time to fit residues: 2.9088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.5981 moved from start: 0.7549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8208 Z= 0.154 Angle : 0.498 8.485 11096 Z= 0.264 Chirality : 0.040 0.145 1296 Planarity : 0.003 0.030 1368 Dihedral : 7.325 58.495 1120 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.45 % Allowed : 18.75 % Favored : 80.80 % 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: 1.71 (0.27), residues: 960 helix: 1.95 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.07 (0.31), residues: 384 *********************** 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 163 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.398 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 outliers start: 4 outliers final: 2 residues processed: 159 average time/residue: 0.4178 time to fit residues: 92.5509 Evaluate side-chains 154 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1938 time to fit residues: 2.4048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.7872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8208 Z= 0.195 Angle : 0.536 8.386 11096 Z= 0.284 Chirality : 0.042 0.155 1296 Planarity : 0.003 0.032 1368 Dihedral : 7.623 59.885 1120 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.56 % Allowed : 18.53 % Favored : 80.92 % 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: 1.52 (0.27), residues: 960 helix: 1.78 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.10 (0.31), residues: 384 *********************** 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 166 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.235 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 outliers start: 5 outliers final: 4 residues processed: 163 average time/residue: 0.4144 time to fit residues: 93.4303 Evaluate side-chains 158 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1727 time to fit residues: 2.9592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 0.0980 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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: 0.5993 moved from start: 0.8039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8208 Z= 0.162 Angle : 0.510 11.699 11096 Z= 0.268 Chirality : 0.041 0.144 1296 Planarity : 0.003 0.031 1368 Dihedral : 7.392 67.529 1120 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.11 % Allowed : 19.08 % Favored : 80.80 % 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: 1.79 (0.27), residues: 960 helix: 2.04 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.09 (0.32), residues: 384 *********************** 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 164 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.4324 time to fit residues: 96.7493 Evaluate side-chains 157 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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: 0.5950 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8208 Z= 0.142 Angle : 0.503 8.862 11096 Z= 0.261 Chirality : 0.040 0.137 1296 Planarity : 0.003 0.038 1368 Dihedral : 7.208 64.111 1120 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 19.64 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.27), residues: 960 helix: 2.23 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.03 (0.32), residues: 384 ********************** 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 163 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.269 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 outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.4365 time to fit residues: 97.6438 Evaluate side-chains 161 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4765 r_free = 0.4765 target = 0.185154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.157952 restraints weight = 27151.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.165063 restraints weight = 10855.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.169386 restraints weight = 5622.222| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.8310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8208 Z= 0.178 Angle : 0.531 8.878 11096 Z= 0.278 Chirality : 0.041 0.149 1296 Planarity : 0.003 0.031 1368 Dihedral : 7.513 63.710 1120 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.11 % Allowed : 19.53 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.27), residues: 960 helix: 2.09 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.04 (0.32), residues: 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4081.85 seconds wall clock time: 72 minutes 56.82 seconds (4376.82 seconds total)