Starting phenix.real_space_refine on Fri Dec 8 04:04:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/12_2023/8t04_40934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/12_2023/8t04_40934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/12_2023/8t04_40934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/12_2023/8t04_40934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/12_2023/8t04_40934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/12_2023/8t04_40934_updated.pdb" } resolution = 2.98 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= 0.003 sd= 0.088 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 Zn 2 6.06 5 P 2 5.49 5 S 44 5.16 5 C 4492 2.51 5 N 1092 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6874 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Time building chain proxies: 4.19, per 1000 atoms: 0.61 Number of scatterers: 6874 At special positions: 0 Unit cell: (72.21, 108.73, 103.75, 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) Zn 2 29.99 S 44 16.00 P 2 15.00 O 1242 8.00 N 1092 7.00 C 4492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 38.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 Proline residue: A 11 - end of helix removed outlier: 3.828A pdb=" N SER A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 31 through 51 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 86 Processing helix chain 'A' and resid 92 through 110 Processing helix chain 'A' and resid 119 through 140 Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.898A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 27 Proline residue: B 11 - end of helix removed outlier: 3.825A pdb=" N SER B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) Proline residue: B 20 - end of helix Processing helix chain 'B' and resid 31 through 51 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 63 through 86 Processing helix chain 'B' and resid 92 through 110 Processing helix chain 'B' and resid 119 through 140 Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 176 through 194 removed outlier: 3.899A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'C' and resid 114 through 116 removed outlier: 6.084A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 47 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.816A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= E, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.357A pdb=" N LYS D 103 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA D 13 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU D 105 " --> pdb=" O ALA D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 85 through 90 removed outlier: 6.567A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= H, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.077A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU E 47 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.813A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= K, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.359A pdb=" N LYS F 103 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA F 13 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU F 105 " --> pdb=" O ALA F 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 85 through 90 removed outlier: 6.565A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 918 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: 1.84 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1024 1.31 - 1.44: 2033 1.44 - 1.56: 3921 1.56 - 1.69: 8 1.69 - 1.82: 72 Bond restraints: 7058 Sorted by residual: bond pdb=" C ARG B 93 " pdb=" N SER B 94 " ideal model delta sigma weight residual 1.335 1.446 -0.111 1.31e-02 5.83e+03 7.19e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.432 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.422 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 7053 not shown) Histogram of bond angle deviations from ideal: 94.97 - 102.98: 51 102.98 - 111.00: 2180 111.00 - 119.01: 4214 119.01 - 127.03: 3027 127.03 - 135.04: 92 Bond angle restraints: 9564 Sorted by residual: angle pdb=" O ARG A 93 " pdb=" C ARG A 93 " pdb=" N SER A 94 " ideal model delta sigma weight residual 122.09 129.02 -6.93 1.04e+00 9.25e-01 4.45e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 110.27 -16.82 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 110.19 -16.74 3.00e+00 1.11e-01 3.12e+01 angle pdb=" N GLU B 90 " pdb=" CA GLU B 90 " pdb=" C GLU B 90 " ideal model delta sigma weight residual 110.07 103.09 6.98 1.26e+00 6.30e-01 3.07e+01 angle pdb=" N GLU A 90 " pdb=" CA GLU A 90 " pdb=" C GLU A 90 " ideal model delta sigma weight residual 110.07 103.11 6.96 1.26e+00 6.30e-01 3.06e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 4126 34.41 - 68.82: 103 68.82 - 103.23: 17 103.23 - 137.64: 2 137.64 - 172.05: 2 Dihedral angle restraints: 4250 sinusoidal: 1788 harmonic: 2462 Sorted by residual: dihedral pdb=" CA HIS F 49 " pdb=" C HIS F 49 " pdb=" N TYR F 50 " pdb=" CA TYR F 50 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA HIS D 49 " pdb=" C HIS D 49 " pdb=" N TYR D 50 " pdb=" CA TYR D 50 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU A 90 " pdb=" C GLU A 90 " pdb=" N PRO A 91 " pdb=" CA PRO A 91 " ideal model delta harmonic sigma weight residual 0.00 26.21 -26.21 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 4247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.983: 1052 0.983 - 1.966: 0 1.966 - 2.949: 0 2.949 - 3.932: 0 3.932 - 4.915: 2 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.91 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1051 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 110 " 0.021 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" CG TRP C 110 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 110 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 110 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 110 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 110 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 110 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 110 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 110 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 110 " -0.021 2.00e-02 2.50e+03 1.18e-02 3.46e+00 pdb=" CG TRP E 110 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 110 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 110 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 110 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 110 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 110 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 93 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C ARG B 93 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG B 93 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 94 " -0.009 2.00e-02 2.50e+03 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1246 2.84 - 3.35: 6740 3.35 - 3.87: 10891 3.87 - 4.38: 14400 4.38 - 4.90: 23581 Nonbonded interactions: 56858 Sorted by model distance: nonbonded pdb=" NH1 ARG D 61 " pdb=" OD2 ASP D 82 " model vdw 2.320 2.520 nonbonded pdb=" NH1 ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 2.320 2.520 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.479 2.520 nonbonded pdb=" NH2 ARG F 61 " pdb=" OE2 GLU F 81 " model vdw 2.479 2.520 nonbonded pdb=" N GLY B 116 " pdb=" O4 LBN B 303 " model vdw 2.483 2.520 ... (remaining 56853 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.950 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.610 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 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 : 0.014 0.111 7058 Z= 0.931 Angle : 1.828 16.817 9564 Z= 1.300 Chirality : 0.230 4.915 1054 Planarity : 0.004 0.027 1156 Dihedral : 16.387 172.049 2666 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.27 % Allowed : 6.81 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.07 (0.29), residues: 840 helix: -1.11 (0.26), residues: 278 sheet: 0.01 (0.40), residues: 166 loop : -0.57 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 110 HIS 0.007 0.002 HIS C 52 PHE 0.021 0.002 PHE B 69 TYR 0.028 0.003 TYR D 91 ARG 0.006 0.001 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.880 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.9213 time to fit residues: 113.6175 Evaluate side-chains 82 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.6487 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7058 Z= 0.228 Angle : 0.597 6.244 9564 Z= 0.310 Chirality : 0.044 0.158 1054 Planarity : 0.004 0.031 1156 Dihedral : 12.366 133.173 1136 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.54 % Allowed : 12.67 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 840 helix: 1.06 (0.28), residues: 292 sheet: 0.04 (0.35), residues: 234 loop : -0.01 (0.41), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 110 HIS 0.004 0.001 HIS D 49 PHE 0.020 0.002 PHE B 42 TYR 0.012 0.001 TYR F 91 ARG 0.002 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.731 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 118 average time/residue: 1.1161 time to fit residues: 139.2444 Evaluate side-chains 100 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.0693 time to fit residues: 1.2769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.0060 chunk 50 optimal weight: 0.0770 chunk 20 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- 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: 0.6453 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7058 Z= 0.133 Angle : 0.503 5.957 9564 Z= 0.260 Chirality : 0.041 0.159 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.860 124.834 1136 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.59 % Allowed : 15.40 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.18 (0.31), residues: 840 helix: 1.84 (0.28), residues: 294 sheet: 0.31 (0.36), residues: 236 loop : 0.29 (0.42), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS C 52 PHE 0.014 0.001 PHE A 43 TYR 0.008 0.001 TYR F 91 ARG 0.008 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.759 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 125 average time/residue: 1.1005 time to fit residues: 145.3932 Evaluate side-chains 105 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.0519 time to fit residues: 2.1516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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: 0.6495 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.191 Angle : 0.518 6.189 9564 Z= 0.266 Chirality : 0.042 0.160 1054 Planarity : 0.004 0.030 1156 Dihedral : 10.857 124.767 1136 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.00 % Allowed : 17.57 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.26 (0.31), residues: 840 helix: 1.86 (0.28), residues: 308 sheet: 0.34 (0.35), residues: 236 loop : 0.31 (0.44), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 110 HIS 0.004 0.001 HIS F 49 PHE 0.018 0.002 PHE A 170 TYR 0.011 0.001 TYR D 91 ARG 0.007 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.717 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 1.0877 time to fit residues: 131.3527 Evaluate side-chains 107 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.0629 time to fit residues: 1.3732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.6523 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7058 Z= 0.246 Angle : 0.543 6.258 9564 Z= 0.279 Chirality : 0.043 0.158 1054 Planarity : 0.004 0.031 1156 Dihedral : 11.043 131.636 1136 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.68 % Allowed : 17.98 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.15 (0.31), residues: 840 helix: 1.69 (0.28), residues: 308 sheet: 0.43 (0.35), residues: 230 loop : 0.22 (0.42), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 110 HIS 0.005 0.001 HIS D 49 PHE 0.021 0.002 PHE A 42 TYR 0.012 0.001 TYR F 91 ARG 0.008 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 0.727 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 122 average time/residue: 1.0201 time to fit residues: 132.8450 Evaluate side-chains 116 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.1069 time to fit residues: 1.2107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6509 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.193 Angle : 0.517 6.098 9564 Z= 0.265 Chirality : 0.042 0.153 1054 Planarity : 0.004 0.035 1156 Dihedral : 10.475 133.144 1136 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 19.07 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.23 (0.31), residues: 840 helix: 1.87 (0.28), residues: 308 sheet: 0.49 (0.35), residues: 230 loop : 0.10 (0.41), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 55 HIS 0.004 0.001 HIS C 52 PHE 0.017 0.002 PHE B 170 TYR 0.010 0.001 TYR D 91 ARG 0.008 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.648 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 112 average time/residue: 1.1025 time to fit residues: 130.7798 Evaluate side-chains 110 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.0608 time to fit residues: 1.2351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.0270 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.6492 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7058 Z= 0.152 Angle : 0.490 6.021 9564 Z= 0.251 Chirality : 0.041 0.151 1054 Planarity : 0.004 0.038 1156 Dihedral : 10.020 130.098 1136 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.13 % Allowed : 19.07 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.30), residues: 840 helix: 2.07 (0.28), residues: 308 sheet: 0.67 (0.35), residues: 230 loop : -0.00 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 55 HIS 0.003 0.001 HIS E 52 PHE 0.019 0.001 PHE A 42 TYR 0.010 0.001 TYR F 91 ARG 0.009 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.683 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 119 average time/residue: 1.0682 time to fit residues: 135.1591 Evaluate side-chains 113 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.0494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 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: 0.6504 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.191 Angle : 0.510 6.097 9564 Z= 0.263 Chirality : 0.042 0.151 1054 Planarity : 0.004 0.036 1156 Dihedral : 9.989 127.556 1136 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.54 % Allowed : 18.39 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.30), residues: 840 helix: 2.00 (0.28), residues: 308 sheet: 0.72 (0.35), residues: 230 loop : -0.06 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 55 HIS 0.003 0.001 HIS F 49 PHE 0.019 0.002 PHE A 170 TYR 0.011 0.001 TYR D 71 ARG 0.008 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.790 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 1.0436 time to fit residues: 133.0522 Evaluate side-chains 110 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.0455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.6499 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7058 Z= 0.193 Angle : 0.516 6.066 9564 Z= 0.265 Chirality : 0.042 0.143 1054 Planarity : 0.004 0.036 1156 Dihedral : 9.914 125.790 1136 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.59 % Allowed : 20.16 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.35 (0.30), residues: 840 helix: 1.98 (0.28), residues: 308 sheet: 0.78 (0.35), residues: 234 loop : -0.07 (0.41), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 55 HIS 0.003 0.001 HIS F 49 PHE 0.019 0.001 PHE A 42 TYR 0.012 0.001 TYR D 71 ARG 0.008 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.762 Fit side-chains outliers start: 19 outliers final: 17 residues processed: 115 average time/residue: 1.0184 time to fit residues: 124.5279 Evaluate side-chains 108 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 0.9892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.0050 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.0070 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 0.3812 ------------------------------------------------------------------------------- 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: 0.6466 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7058 Z= 0.135 Angle : 0.481 5.948 9564 Z= 0.249 Chirality : 0.040 0.142 1054 Planarity : 0.004 0.038 1156 Dihedral : 9.572 122.210 1136 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.72 % Allowed : 20.03 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.64 (0.31), residues: 840 helix: 2.34 (0.28), residues: 304 sheet: 0.95 (0.36), residues: 234 loop : -0.04 (0.41), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 55 HIS 0.003 0.001 HIS E 52 PHE 0.024 0.001 PHE A 170 TYR 0.011 0.001 TYR F 71 ARG 0.008 0.000 ARG A 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.770 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 1.0094 time to fit residues: 134.5726 Evaluate side-chains 124 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.0658 time to fit residues: 1.9863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.176153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125474 restraints weight = 6993.800| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.43 r_work: 0.3349 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7058 Z= 0.155 Angle : 0.493 6.008 9564 Z= 0.254 Chirality : 0.041 0.141 1054 Planarity : 0.004 0.039 1156 Dihedral : 9.531 120.624 1136 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.23 % Allowed : 21.66 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.66 (0.31), residues: 840 helix: 2.41 (0.28), residues: 294 sheet: 0.97 (0.36), residues: 234 loop : -0.02 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 55 HIS 0.003 0.001 HIS C 52 PHE 0.021 0.001 PHE B 42 TYR 0.011 0.001 TYR D 71 ARG 0.009 0.001 ARG A 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.91 seconds wall clock time: 49 minutes 23.49 seconds (2963.49 seconds total)