Starting phenix.real_space_refine on Mon Dec 11 04:05:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkk_12442/12_2023/7nkk_12442.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkk_12442/12_2023/7nkk_12442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkk_12442/12_2023/7nkk_12442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkk_12442/12_2023/7nkk_12442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkk_12442/12_2023/7nkk_12442.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkk_12442/12_2023/7nkk_12442.pdb" } resolution = 3.6 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= 0.001 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 5345 2.51 5 N 1391 2.21 5 O 1533 1.98 5 H 8376 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 74": "OE1" <-> "OE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "Q PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 32": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16671 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 2, 'TRANS': 11} Chain: "G" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3794 Classifications: {'peptide': 246} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 236} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "M" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "P" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1224 Classifications: {'peptide': 86} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "Q" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "R" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "S" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "T" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Time building chain proxies: 7.99, per 1000 atoms: 0.48 Number of scatterers: 16671 At special positions: 0 Unit cell: (66.4, 78.02, 149.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 1533 8.00 N 1391 7.00 C 5345 6.00 H 8376 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: 16.47 Conformation dependent library (CDL) restraints added in 2.2 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 74.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'G' and resid 19 through 43 Processing helix chain 'G' and resid 43 through 60 Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 91 through 111 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.620A pdb=" N LEU G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 164 Processing helix chain 'G' and resid 227 through 268 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 91 through 99 Processing helix chain 'H' and resid 103 through 118 Processing helix chain 'L' and resid 4 through 46 Processing helix chain 'L' and resid 49 through 81 removed outlier: 4.894A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.580A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 4.155A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 81 removed outlier: 3.696A pdb=" N PHE M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.691A pdb=" N ILE M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.653A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.532A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.599A pdb=" N THR N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL N 61 " --> pdb=" O PHE N 57 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.515A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 3.974A pdb=" N PHE O 54 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.627A pdb=" N ASN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 Processing helix chain 'P' and resid 49 through 81 removed outlier: 4.424A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.574A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.520A pdb=" N PHE Q 54 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.558A pdb=" N ALA Q 66 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 46 Processing helix chain 'R' and resid 49 through 80 removed outlier: 4.375A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.883A pdb=" N ILE R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 removed outlier: 3.737A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 80 removed outlier: 3.600A pdb=" N PHE S 54 " --> pdb=" O GLN S 50 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.755A pdb=" N ALA S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 Processing helix chain 'T' and resid 49 through 81 removed outlier: 3.794A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.094A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 11.260A pdb=" N GLU C 534 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N GLU G 207 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU C 536 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU G 209 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL C 538 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL G 211 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL C 540 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA G 198 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU G 189 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA G 200 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE G 187 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG G 202 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE G 185 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU G 136 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 223 through 225 removed outlier: 6.178A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU G 225 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 32 through 34 712 hydrogen bonds defined for protein. 2103 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: 7.25 Time building geometry restraints manager: 16.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8375 1.03 - 1.23: 112 1.23 - 1.43: 3327 1.43 - 1.62: 4946 1.62 - 1.82: 51 Bond restraints: 16811 Sorted by residual: bond pdb=" CG1 ILE Q 20 " pdb=" CD1 ILE Q 20 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.29e+00 bond pdb=" CG1 ILE M 20 " pdb=" CD1 ILE M 20 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" CG1 ILE R 30 " pdb=" CD1 ILE R 30 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" SD MET R 21 " pdb=" CE MET R 21 " ideal model delta sigma weight residual 1.791 1.767 0.024 2.50e-02 1.60e+03 9.12e-01 bond pdb=" CG LEU Q 19 " pdb=" CD1 LEU Q 19 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.81e-01 ... (remaining 16806 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.87: 275 106.87 - 113.66: 19905 113.66 - 120.45: 5947 120.45 - 127.23: 4252 127.23 - 134.02: 58 Bond angle restraints: 30437 Sorted by residual: angle pdb=" CB MET R 21 " pdb=" CG MET R 21 " pdb=" SD MET R 21 " ideal model delta sigma weight residual 112.70 120.45 -7.75 3.00e+00 1.11e-01 6.68e+00 angle pdb=" C ILE R 20 " pdb=" N MET R 21 " pdb=" CA MET R 21 " ideal model delta sigma weight residual 121.14 117.37 3.77 1.75e+00 3.27e-01 4.63e+00 angle pdb=" CG MET S 21 " pdb=" SD MET S 21 " pdb=" CE MET S 21 " ideal model delta sigma weight residual 100.90 104.93 -4.03 2.20e+00 2.07e-01 3.36e+00 angle pdb=" C PHE T 74 " pdb=" N MET T 75 " pdb=" CA MET T 75 " ideal model delta sigma weight residual 120.29 117.75 2.54 1.42e+00 4.96e-01 3.19e+00 angle pdb=" CB MET L 21 " pdb=" CG MET L 21 " pdb=" SD MET L 21 " ideal model delta sigma weight residual 112.70 118.04 -5.34 3.00e+00 1.11e-01 3.17e+00 ... (remaining 30432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6725 17.18 - 34.36: 618 34.36 - 51.55: 105 51.55 - 68.73: 14 68.73 - 85.91: 6 Dihedral angle restraints: 7468 sinusoidal: 3887 harmonic: 3581 Sorted by residual: dihedral pdb=" CA VAL G 115 " pdb=" C VAL G 115 " pdb=" N LEU G 116 " pdb=" CA LEU G 116 " ideal model delta harmonic sigma weight residual -180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP G 227 " pdb=" CB ASP G 227 " pdb=" CG ASP G 227 " pdb=" OD1 ASP G 227 " ideal model delta sinusoidal sigma weight residual -30.00 -84.98 54.98 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CB GLU R 65 " pdb=" CG GLU R 65 " pdb=" CD GLU R 65 " pdb=" OE1 GLU R 65 " ideal model delta sinusoidal sigma weight residual 0.00 -83.37 83.37 1 3.00e+01 1.11e-03 9.43e+00 ... (remaining 7465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 885 0.030 - 0.061: 247 0.061 - 0.091: 136 0.091 - 0.122: 51 0.122 - 0.152: 6 Chirality restraints: 1325 Sorted by residual: chirality pdb=" CA ILE G 185 " pdb=" N ILE G 185 " pdb=" C ILE G 185 " pdb=" CB ILE G 185 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE O 20 " pdb=" N ILE O 20 " pdb=" C ILE O 20 " pdb=" CB ILE O 20 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA PRO H 36 " pdb=" N PRO H 36 " pdb=" C PRO H 36 " pdb=" CB PRO H 36 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1322 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE N 70 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C ILE N 70 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE N 70 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN N 71 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 35 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO H 36 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 36 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 36 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET R 21 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C MET R 21 " -0.025 2.00e-02 2.50e+03 pdb=" O MET R 21 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY R 22 " 0.008 2.00e-02 2.50e+03 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.20: 1100 2.20 - 2.80: 35044 2.80 - 3.40: 50710 3.40 - 4.00: 64280 4.00 - 4.60: 100622 Nonbonded interactions: 251756 Sorted by model distance: nonbonded pdb=" OD1 ASN Q 71 " pdb=" HH TYR R 68 " model vdw 1.594 1.850 nonbonded pdb=" OE1 GLU H 104 " pdb=" H GLU H 104 " model vdw 1.607 1.850 nonbonded pdb=" OE1 GLU G 143 " pdb=" H GLU G 143 " model vdw 1.625 1.850 nonbonded pdb=" HG SER G 192 " pdb=" OG SER G 195 " model vdw 1.625 1.850 nonbonded pdb=" O PHE S 78 " pdb=" HG1 THR S 82 " model vdw 1.626 1.850 ... (remaining 251751 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 'L' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'M' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'N' selection = (chain 'O' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'P' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'Q' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'R' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'S' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'T' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) } 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: 9.410 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: 0.290 Extract box with map and model: 25.420 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 61.610 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.003 0.044 8435 Z= 0.201 Angle : 0.509 7.752 11434 Z= 0.272 Chirality : 0.040 0.152 1325 Planarity : 0.004 0.036 1510 Dihedral : 13.865 85.910 2942 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.95 (0.26), residues: 1117 helix: 1.82 (0.19), residues: 820 sheet: -0.88 (0.54), residues: 86 loop : 0.36 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 109 HIS 0.002 0.001 HIS G 65 PHE 0.019 0.001 PHE P 54 TYR 0.007 0.001 TYR G 46 ARG 0.003 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3568 time to fit residues: 33.2139 Evaluate side-chains 44 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.0000 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- 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: 0.7976 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8435 Z= 0.240 Angle : 0.538 6.268 11434 Z= 0.283 Chirality : 0.040 0.134 1325 Planarity : 0.004 0.037 1510 Dihedral : 3.671 18.336 1200 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.50 % Allowed : 5.28 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.68 (0.25), residues: 1117 helix: 2.43 (0.18), residues: 832 sheet: -0.79 (0.54), residues: 84 loop : 0.18 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 109 HIS 0.001 0.001 HIS H 38 PHE 0.015 0.001 PHE P 54 TYR 0.007 0.001 TYR M 68 ARG 0.003 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.3696 time to fit residues: 30.4759 Evaluate side-chains 45 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2349 time to fit residues: 2.8578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 33 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.7956 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8435 Z= 0.181 Angle : 0.485 5.299 11434 Z= 0.254 Chirality : 0.040 0.140 1325 Planarity : 0.003 0.037 1510 Dihedral : 3.598 17.895 1200 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.38 % Allowed : 7.66 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.26), residues: 1117 helix: 2.82 (0.18), residues: 833 sheet: -0.68 (0.55), residues: 84 loop : 0.33 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 16 HIS 0.001 0.001 HIS G 184 PHE 0.012 0.001 PHE Q 74 TYR 0.007 0.001 TYR M 68 ARG 0.002 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 1.146 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.3651 time to fit residues: 27.2257 Evaluate side-chains 46 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1857 time to fit residues: 1.8428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7976 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8435 Z= 0.219 Angle : 0.509 7.304 11434 Z= 0.264 Chirality : 0.040 0.164 1325 Planarity : 0.003 0.038 1510 Dihedral : 3.624 18.178 1200 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.38 % Allowed : 9.30 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.25), residues: 1117 helix: 2.90 (0.17), residues: 834 sheet: -0.71 (0.56), residues: 84 loop : 0.35 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 16 HIS 0.002 0.001 HIS G 65 PHE 0.014 0.001 PHE Q 74 TYR 0.008 0.001 TYR M 68 ARG 0.003 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.3840 time to fit residues: 28.0743 Evaluate side-chains 45 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2596 time to fit residues: 2.3584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8435 Z= 0.250 Angle : 0.517 6.894 11434 Z= 0.270 Chirality : 0.040 0.139 1325 Planarity : 0.004 0.038 1510 Dihedral : 3.666 18.639 1200 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.50 % Allowed : 9.80 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.25), residues: 1117 helix: 2.93 (0.17), residues: 834 sheet: -0.80 (0.56), residues: 85 loop : 0.37 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 16 HIS 0.002 0.001 HIS G 65 PHE 0.014 0.001 PHE R 74 TYR 0.008 0.001 TYR M 68 ARG 0.003 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 47 average time/residue: 0.3741 time to fit residues: 27.3167 Evaluate side-chains 42 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1966 time to fit residues: 1.8029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8435 Z= 0.223 Angle : 0.509 7.475 11434 Z= 0.263 Chirality : 0.040 0.138 1325 Planarity : 0.004 0.038 1510 Dihedral : 3.644 18.544 1200 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.50 % Allowed : 10.18 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.25), residues: 1117 helix: 2.99 (0.17), residues: 834 sheet: -0.74 (0.56), residues: 85 loop : 0.40 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 16 HIS 0.001 0.001 HIS H 38 PHE 0.018 0.001 PHE Q 74 TYR 0.007 0.001 TYR G 92 ARG 0.003 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 43 average time/residue: 0.4109 time to fit residues: 27.0604 Evaluate side-chains 40 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 GLN S 6 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8435 Z= 0.259 Angle : 0.522 7.373 11434 Z= 0.273 Chirality : 0.040 0.139 1325 Planarity : 0.004 0.039 1510 Dihedral : 3.707 19.347 1200 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.63 % Allowed : 10.93 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.25), residues: 1117 helix: 2.93 (0.17), residues: 833 sheet: -0.62 (0.57), residues: 81 loop : 0.24 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 16 HIS 0.004 0.001 HIS G 65 PHE 0.012 0.001 PHE Q 74 TYR 0.009 0.001 TYR G 92 ARG 0.003 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.3737 time to fit residues: 25.1864 Evaluate side-chains 42 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2329 time to fit residues: 2.3469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8435 Z= 0.207 Angle : 0.512 7.171 11434 Z= 0.263 Chirality : 0.040 0.135 1325 Planarity : 0.004 0.038 1510 Dihedral : 3.661 18.862 1200 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.13 % Allowed : 11.68 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.25), residues: 1117 helix: 3.01 (0.17), residues: 834 sheet: -0.56 (0.58), residues: 81 loop : 0.30 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 16 HIS 0.001 0.001 HIS H 38 PHE 0.012 0.001 PHE R 74 TYR 0.007 0.001 TYR G 92 ARG 0.003 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.417 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.3815 time to fit residues: 24.8460 Evaluate side-chains 41 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1969 time to fit residues: 1.9562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8008 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8435 Z= 0.265 Angle : 0.545 8.777 11434 Z= 0.280 Chirality : 0.040 0.140 1325 Planarity : 0.004 0.039 1510 Dihedral : 3.713 19.316 1200 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.13 % Allowed : 12.19 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.25), residues: 1117 helix: 2.91 (0.17), residues: 834 sheet: -0.63 (0.59), residues: 81 loop : 0.27 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 16 HIS 0.002 0.001 HIS H 38 PHE 0.012 0.001 PHE R 74 TYR 0.009 0.001 TYR G 92 ARG 0.003 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.679 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.3823 time to fit residues: 24.5062 Evaluate side-chains 40 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8435 Z= 0.295 Angle : 0.550 7.838 11434 Z= 0.286 Chirality : 0.040 0.148 1325 Planarity : 0.004 0.038 1510 Dihedral : 3.783 19.829 1200 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.25), residues: 1117 helix: 2.82 (0.17), residues: 834 sheet: -0.72 (0.58), residues: 81 loop : 0.18 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 16 HIS 0.002 0.001 HIS H 38 PHE 0.011 0.001 PHE R 74 TYR 0.010 0.001 TYR M 68 ARG 0.004 0.000 ARG R 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.248 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.3869 time to fit residues: 24.2698 Evaluate side-chains 40 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.075291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062288 restraints weight = 89273.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.064458 restraints weight = 34624.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.065784 restraints weight = 18120.051| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8435 Z= 0.208 Angle : 0.522 8.088 11434 Z= 0.265 Chirality : 0.040 0.149 1325 Planarity : 0.004 0.039 1510 Dihedral : 3.674 19.105 1200 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.25), residues: 1117 helix: 3.18 (0.17), residues: 806 sheet: -0.66 (0.58), residues: 81 loop : 0.12 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 16 HIS 0.001 0.001 HIS H 38 PHE 0.017 0.001 PHE Q 74 TYR 0.007 0.001 TYR G 92 ARG 0.002 0.000 ARG R 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3327.52 seconds wall clock time: 59 minutes 59.92 seconds (3599.92 seconds total)