Starting phenix.real_space_refine on Fri Mar 15 17:08:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/03_2024/6yov_10864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/03_2024/6yov_10864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/03_2024/6yov_10864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/03_2024/6yov_10864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/03_2024/6yov_10864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/03_2024/6yov_10864_updated.pdb" } resolution = 3.42 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= 0.005 sd= 0.044 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 P 261 5.49 5 S 19 5.16 5 C 6892 2.51 5 N 2327 2.21 5 O 2799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12298 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2662 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2706 Classifications: {'DNA': 131} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 130} Chain: "K" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 272 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 625 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 6.22, per 1000 atoms: 0.51 Number of scatterers: 12298 At special positions: 0 Unit cell: (104.06, 116.96, 129.86, 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 19 16.00 P 261 15.00 O 2799 8.00 N 2327 7.00 C 6892 6.00 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 997.4 milliseconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1550 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 0 sheets defined 64.1% alpha, 0.0% beta 129 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.897A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'B' and resid 26 through 29 Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 51 through 76 Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.145A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 21 No H-bonds generated for 'chain 'C' and resid 18 through 21' Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 48 through 73 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 39 through 48 Processing helix chain 'D' and resid 57 through 84 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 105 through 122 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 65 through 78 removed outlier: 3.768A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 51 through 76 Processing helix chain 'F' and resid 84 through 94 removed outlier: 3.903A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.247A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 94 through 97 No H-bonds generated for 'chain 'G' and resid 94 through 97' Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 123 removed outlier: 3.961A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 159 Processing helix chain 'K' and resid 164 through 175 Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 194 through 207 Proline residue: K 202 - end of helix Processing helix chain 'L' and resid 47 through 60 removed outlier: 3.566A pdb=" N GLY L 54 " --> pdb=" O VAL L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 80 Processing helix chain 'L' and resid 84 through 104 Proline residue: L 89 - end of helix 398 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 330 hydrogen bonds 660 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 4.07 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2001 1.32 - 1.45: 4464 1.45 - 1.57: 6014 1.57 - 1.69: 522 1.69 - 1.81: 34 Bond restraints: 13035 Sorted by residual: bond pdb=" CA ASN F 26 " pdb=" C ASN F 26 " ideal model delta sigma weight residual 1.522 1.601 -0.079 1.37e-02 5.33e+03 3.32e+01 bond pdb=" O3' DT J 84 " pdb=" P DG J 85 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.23e+01 bond pdb=" CD ARG B 40 " pdb=" NE ARG B 40 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.88e+00 bond pdb=" NE ARG B 24 " pdb=" CZ ARG B 24 " ideal model delta sigma weight residual 1.326 1.360 -0.034 1.10e-02 8.26e+03 9.81e+00 ... (remaining 13030 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.35: 1263 105.35 - 112.48: 7071 112.48 - 119.61: 3818 119.61 - 126.74: 5842 126.74 - 133.86: 667 Bond angle restraints: 18661 Sorted by residual: angle pdb=" N LYS L 42 " pdb=" CA LYS L 42 " pdb=" C LYS L 42 " ideal model delta sigma weight residual 110.53 120.03 -9.50 1.29e+00 6.01e-01 5.43e+01 angle pdb=" C HIS L 105 " pdb=" N PRO L 106 " pdb=" CA PRO L 106 " ideal model delta sigma weight residual 119.47 127.73 -8.26 1.16e+00 7.43e-01 5.07e+01 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.56 126.55 -6.99 1.02e+00 9.61e-01 4.70e+01 angle pdb=" C HIS H 50 " pdb=" N PRO H 51 " pdb=" CA PRO H 51 " ideal model delta sigma weight residual 119.56 126.48 -6.92 1.02e+00 9.61e-01 4.61e+01 angle pdb=" C LEU H 103 " pdb=" N PRO H 104 " pdb=" CA PRO H 104 " ideal model delta sigma weight residual 120.31 126.68 -6.37 9.80e-01 1.04e+00 4.23e+01 ... (remaining 18656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5050 17.90 - 35.81: 948 35.81 - 53.71: 831 53.71 - 71.61: 260 71.61 - 89.52: 12 Dihedral angle restraints: 7101 sinusoidal: 4631 harmonic: 2470 Sorted by residual: dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C ASN F 26 " pdb=" N ASN F 26 " pdb=" CA ASN F 26 " pdb=" CB ASN F 26 " ideal model delta harmonic sigma weight residual -122.60 -131.46 8.86 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 7098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1339 0.060 - 0.120: 573 0.120 - 0.180: 133 0.180 - 0.240: 17 0.240 - 0.300: 5 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CA GLN L 61 " pdb=" N GLN L 61 " pdb=" C GLN L 61 " pdb=" CB GLN L 61 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA LEU E 66 " pdb=" N LEU E 66 " pdb=" C LEU E 66 " pdb=" CB LEU E 66 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG L 88 " pdb=" N ARG L 88 " pdb=" C ARG L 88 " pdb=" CB ARG L 88 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2064 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 55 " 0.074 2.00e-02 2.50e+03 4.04e-02 3.27e+01 pdb=" CG TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 55 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 55 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 55 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 55 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 55 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 41 " 0.072 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR H 41 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 41 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR H 41 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR H 41 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR H 41 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 41 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 41 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 55 " -0.064 2.00e-02 2.50e+03 3.32e-02 2.20e+01 pdb=" CG TYR E 55 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 55 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 55 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 55 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 55 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 55 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 55 " -0.045 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 4214 2.90 - 3.40: 10798 3.40 - 3.90: 24233 3.90 - 4.40: 28470 4.40 - 4.90: 37137 Nonbonded interactions: 104852 Sorted by model distance: nonbonded pdb=" N GLU G 42 " pdb=" OE1 GLU G 42 " model vdw 2.395 2.520 nonbonded pdb=" O2 DT I 125 " pdb=" OG SER L 72 " model vdw 2.399 2.440 nonbonded pdb=" OG SER G 19 " pdb=" O PHE G 26 " model vdw 2.404 2.440 nonbonded pdb=" OG1 THR C 77 " pdb=" OP1 DG J 133 " model vdw 2.407 2.440 nonbonded pdb=" NH2 ARG A 54 " pdb=" OH TYR A 55 " model vdw 2.462 2.520 ... (remaining 104847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 23 through 102 or resid 201)) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 9 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 34 through 125 or resid 201)) selection = (chain 'H' and (resid 34 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.230 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.880 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.011 0.091 13035 Z= 0.712 Angle : 1.137 9.504 18661 Z= 0.776 Chirality : 0.067 0.300 2067 Planarity : 0.009 0.046 1480 Dihedral : 25.194 89.518 5551 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 878 helix: 0.78 (0.18), residues: 650 sheet: None (None), residues: 0 loop : 0.34 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.007 TRP L 79 HIS 0.010 0.002 HIS D 110 PHE 0.046 0.010 PHE D 71 TYR 0.074 0.010 TYR A 55 ARG 0.010 0.001 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8372 (m-30) cc_final: 0.8108 (m-30) REVERT: A 121 MET cc_start: 0.8920 (mmm) cc_final: 0.8655 (mmm) REVERT: A 124 ASP cc_start: 0.8083 (m-30) cc_final: 0.7841 (m-30) REVERT: C 26 PHE cc_start: 0.8846 (m-10) cc_final: 0.8641 (m-80) REVERT: C 40 TYR cc_start: 0.8856 (m-80) cc_final: 0.8583 (m-80) REVERT: C 102 THR cc_start: 0.8545 (m) cc_final: 0.8342 (p) REVERT: D 72 GLU cc_start: 0.8602 (tt0) cc_final: 0.8346 (tp30) REVERT: E 94 GLN cc_start: 0.9044 (tt0) cc_final: 0.8801 (tt0) REVERT: E 120 ILE cc_start: 0.9443 (mm) cc_final: 0.9156 (mt) REVERT: G 74 ASN cc_start: 0.9213 (m-40) cc_final: 0.8900 (t0) REVERT: G 102 THR cc_start: 0.8998 (m) cc_final: 0.8769 (p) REVERT: H 52 ASP cc_start: 0.8663 (p0) cc_final: 0.8433 (p0) REVERT: H 106 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9135 (tt0) REVERT: H 114 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8213 (mm-30) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2255 time to fit residues: 113.1942 Evaluate side-chains 250 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13035 Z= 0.273 Angle : 0.643 11.143 18661 Z= 0.370 Chirality : 0.038 0.160 2067 Planarity : 0.005 0.057 1480 Dihedral : 28.431 74.164 3881 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 4.91 % Allowed : 18.21 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.27), residues: 878 helix: 2.27 (0.20), residues: 658 sheet: None (None), residues: 0 loop : 0.09 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 51 HIS 0.010 0.002 HIS F 76 PHE 0.027 0.003 PHE B 62 TYR 0.023 0.002 TYR H 41 ARG 0.006 0.001 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 283 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASN cc_start: 0.7153 (m-40) cc_final: 0.6931 (m-40) REVERT: E 81 THR cc_start: 0.7768 (p) cc_final: 0.7238 (p) REVERT: E 91 MET cc_start: 0.8874 (mmm) cc_final: 0.8649 (mmt) REVERT: F 27 ILE cc_start: 0.9453 (tp) cc_final: 0.9227 (tp) REVERT: G 37 LYS cc_start: 0.7593 (ttpp) cc_final: 0.7378 (mtpt) REVERT: G 40 TYR cc_start: 0.8715 (m-80) cc_final: 0.8481 (m-80) REVERT: G 57 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8958 (tt0) REVERT: G 74 ASN cc_start: 0.9269 (m-40) cc_final: 0.8877 (t0) REVERT: G 102 THR cc_start: 0.9209 (m) cc_final: 0.9001 (p) outliers start: 34 outliers final: 23 residues processed: 299 average time/residue: 0.2248 time to fit residues: 95.4497 Evaluate side-chains 259 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 236 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 0.0870 chunk 102 optimal weight: 50.0000 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 overall best weight: 4.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN E 94 GLN G 25 GLN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13035 Z= 0.320 Angle : 0.637 10.924 18661 Z= 0.367 Chirality : 0.038 0.161 2067 Planarity : 0.005 0.046 1480 Dihedral : 28.690 74.126 3881 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 6.65 % Allowed : 20.52 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.27), residues: 878 helix: 2.30 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -0.06 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 79 HIS 0.014 0.002 HIS G 32 PHE 0.014 0.002 PHE E 68 TYR 0.014 0.002 TYR H 41 ARG 0.014 0.001 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8970 (tm-30) REVERT: D 116 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9017 (p) REVERT: E 91 MET cc_start: 0.8953 (mmm) cc_final: 0.8686 (mmt) REVERT: E 124 ASP cc_start: 0.8297 (m-30) cc_final: 0.7831 (m-30) REVERT: G 40 TYR cc_start: 0.8988 (m-80) cc_final: 0.8775 (m-80) REVERT: G 73 ASP cc_start: 0.8510 (m-30) cc_final: 0.8242 (m-30) REVERT: G 74 ASN cc_start: 0.9277 (m-40) cc_final: 0.8846 (t0) REVERT: G 105 GLN cc_start: 0.9363 (mp10) cc_final: 0.9051 (mp10) outliers start: 46 outliers final: 31 residues processed: 263 average time/residue: 0.2371 time to fit residues: 89.2228 Evaluate side-chains 246 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN F 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13035 Z= 0.312 Angle : 0.638 12.298 18661 Z= 0.365 Chirality : 0.037 0.150 2067 Planarity : 0.005 0.047 1480 Dihedral : 28.594 74.065 3881 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 6.36 % Allowed : 22.69 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.28), residues: 878 helix: 2.30 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.13 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 51 HIS 0.008 0.001 HIS B 76 PHE 0.024 0.002 PHE D 71 TYR 0.014 0.002 TYR B 89 ARG 0.004 0.000 ARG L 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 229 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8370 (mmm) cc_final: 0.7850 (mmm) REVERT: B 89 TYR cc_start: 0.8796 (m-80) cc_final: 0.8406 (m-80) REVERT: D 48 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8918 (tm-30) REVERT: D 116 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9000 (p) REVERT: E 51 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8578 (tp30) REVERT: G 73 ASP cc_start: 0.8708 (m-30) cc_final: 0.8418 (m-30) REVERT: G 74 ASN cc_start: 0.9218 (m-40) cc_final: 0.8845 (t0) REVERT: G 85 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8836 (tp-100) REVERT: G 102 THR cc_start: 0.9372 (m) cc_final: 0.9032 (p) REVERT: G 105 GLN cc_start: 0.9351 (mp10) cc_final: 0.9020 (mp10) outliers start: 44 outliers final: 29 residues processed: 249 average time/residue: 0.2218 time to fit residues: 79.7733 Evaluate side-chains 244 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.0770 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- 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: 0.8496 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13035 Z= 0.264 Angle : 0.628 12.825 18661 Z= 0.357 Chirality : 0.037 0.337 2067 Planarity : 0.004 0.053 1480 Dihedral : 28.551 74.087 3881 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.91 % Allowed : 23.84 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.28), residues: 878 helix: 2.20 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.03 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 51 HIS 0.007 0.001 HIS B 76 PHE 0.009 0.001 PHE E 79 TYR 0.023 0.002 TYR B 89 ARG 0.007 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 236 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9392 (p) cc_final: 0.9188 (t) REVERT: B 85 MET cc_start: 0.8216 (mmm) cc_final: 0.7644 (mmm) REVERT: B 89 TYR cc_start: 0.8423 (m-80) cc_final: 0.8015 (m-80) REVERT: D 48 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8876 (tm-30) REVERT: D 116 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9058 (p) REVERT: E 51 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8603 (tp30) REVERT: E 124 ASP cc_start: 0.8388 (m-30) cc_final: 0.8082 (m-30) REVERT: G 73 ASP cc_start: 0.8790 (m-30) cc_final: 0.8588 (m-30) REVERT: G 74 ASN cc_start: 0.9214 (m-40) cc_final: 0.8868 (t0) REVERT: G 85 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8787 (tp-100) REVERT: G 105 GLN cc_start: 0.9344 (mp10) cc_final: 0.8901 (mp10) outliers start: 34 outliers final: 27 residues processed: 254 average time/residue: 0.2256 time to fit residues: 82.4895 Evaluate side-chains 239 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13035 Z= 0.246 Angle : 0.638 14.948 18661 Z= 0.356 Chirality : 0.036 0.170 2067 Planarity : 0.004 0.051 1480 Dihedral : 28.526 73.695 3881 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 5.06 % Allowed : 26.45 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.28), residues: 878 helix: 2.22 (0.20), residues: 646 sheet: None (None), residues: 0 loop : 0.08 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 51 HIS 0.004 0.001 HIS F 76 PHE 0.007 0.001 PHE L 48 TYR 0.021 0.002 TYR B 89 ARG 0.007 0.000 ARG L 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8197 (mmm) cc_final: 0.7529 (mmm) REVERT: B 89 TYR cc_start: 0.8332 (m-80) cc_final: 0.7852 (m-80) REVERT: D 48 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8863 (tm-30) REVERT: D 116 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9062 (p) REVERT: E 51 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8683 (tp30) REVERT: G 73 ASP cc_start: 0.8810 (m-30) cc_final: 0.8515 (m-30) REVERT: G 74 ASN cc_start: 0.9224 (m-40) cc_final: 0.8874 (t0) REVERT: G 85 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8753 (tp-100) REVERT: G 105 GLN cc_start: 0.9321 (mp10) cc_final: 0.8992 (mp10) outliers start: 35 outliers final: 28 residues processed: 247 average time/residue: 0.2181 time to fit residues: 78.3882 Evaluate side-chains 241 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 0.1980 chunk 92 optimal weight: 8.9990 chunk 108 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13035 Z= 0.190 Angle : 0.614 13.477 18661 Z= 0.344 Chirality : 0.035 0.177 2067 Planarity : 0.004 0.068 1480 Dihedral : 28.402 73.967 3881 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.76 % Allowed : 27.75 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.28), residues: 878 helix: 2.35 (0.20), residues: 639 sheet: None (None), residues: 0 loop : 0.05 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 51 HIS 0.004 0.001 HIS F 76 PHE 0.025 0.001 PHE D 71 TYR 0.011 0.001 TYR C 40 ARG 0.007 0.000 ARG L 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 232 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.7992 (mmm) cc_final: 0.7737 (mmm) REVERT: D 48 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8843 (tm-30) REVERT: D 116 THR cc_start: 0.9424 (OUTLIER) cc_final: 0.9081 (p) REVERT: E 51 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8520 (tp30) REVERT: E 124 ASP cc_start: 0.8373 (m-30) cc_final: 0.8160 (m-30) REVERT: G 73 ASP cc_start: 0.8787 (m-30) cc_final: 0.8493 (m-30) REVERT: G 74 ASN cc_start: 0.9112 (m-40) cc_final: 0.8880 (t0) REVERT: G 85 GLN cc_start: 0.9154 (tp-100) cc_final: 0.8783 (tp-100) REVERT: G 105 GLN cc_start: 0.9191 (mp10) cc_final: 0.8870 (mp10) outliers start: 26 outliers final: 19 residues processed: 245 average time/residue: 0.2193 time to fit residues: 77.6934 Evaluate side-chains 239 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 219 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS B 76 HIS ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13035 Z= 0.216 Angle : 0.633 13.510 18661 Z= 0.355 Chirality : 0.036 0.252 2067 Planarity : 0.004 0.070 1480 Dihedral : 28.362 74.583 3881 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.32 % Allowed : 27.89 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.28), residues: 878 helix: 2.31 (0.20), residues: 638 sheet: None (None), residues: 0 loop : 0.15 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 51 HIS 0.003 0.001 HIS G 83 PHE 0.015 0.001 PHE E 79 TYR 0.012 0.001 TYR C 40 ARG 0.005 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7842 (m-30) cc_final: 0.7552 (m-30) REVERT: B 85 MET cc_start: 0.8012 (mmm) cc_final: 0.7740 (mmm) REVERT: D 48 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8894 (tm-30) REVERT: D 63 MET cc_start: 0.9000 (mmm) cc_final: 0.8745 (mmm) REVERT: E 51 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8503 (tp30) REVERT: E 77 GLN cc_start: 0.9138 (tp40) cc_final: 0.8878 (tm-30) REVERT: E 124 ASP cc_start: 0.8374 (m-30) cc_final: 0.8172 (m-30) REVERT: G 73 ASP cc_start: 0.8827 (m-30) cc_final: 0.8530 (m-30) REVERT: G 74 ASN cc_start: 0.9087 (m-40) cc_final: 0.8856 (t0) REVERT: G 85 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8804 (tp-100) REVERT: G 105 GLN cc_start: 0.9244 (mp10) cc_final: 0.8935 (mp10) outliers start: 23 outliers final: 19 residues processed: 238 average time/residue: 0.2237 time to fit residues: 76.8437 Evaluate side-chains 235 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 216 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13035 Z= 0.299 Angle : 0.668 14.294 18661 Z= 0.376 Chirality : 0.037 0.231 2067 Planarity : 0.005 0.070 1480 Dihedral : 28.452 74.822 3881 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.05 % Allowed : 27.31 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.28), residues: 878 helix: 2.26 (0.21), residues: 640 sheet: None (None), residues: 0 loop : 0.04 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 51 HIS 0.005 0.001 HIS D 110 PHE 0.023 0.002 PHE D 71 TYR 0.017 0.002 TYR B 89 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8147 (mmm) cc_final: 0.7873 (mmm) REVERT: D 48 GLN cc_start: 0.9326 (tm-30) cc_final: 0.9079 (tm-30) REVERT: D 112 VAL cc_start: 0.9575 (t) cc_final: 0.9333 (p) REVERT: D 116 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9223 (p) REVERT: E 51 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8573 (tp30) REVERT: G 73 ASP cc_start: 0.8906 (m-30) cc_final: 0.8640 (m-30) REVERT: G 74 ASN cc_start: 0.9160 (m-40) cc_final: 0.8878 (t0) REVERT: G 85 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8785 (tp-100) REVERT: G 105 GLN cc_start: 0.9301 (mp10) cc_final: 0.8991 (mp10) REVERT: H 114 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8505 (tp30) outliers start: 28 outliers final: 24 residues processed: 225 average time/residue: 0.2222 time to fit residues: 72.7524 Evaluate side-chains 228 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 112 optimal weight: 20.0000 chunk 103 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13035 Z= 0.279 Angle : 0.677 13.489 18661 Z= 0.379 Chirality : 0.037 0.219 2067 Planarity : 0.005 0.069 1480 Dihedral : 28.454 74.315 3881 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.90 % Allowed : 28.18 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.28), residues: 878 helix: 2.25 (0.21), residues: 637 sheet: None (None), residues: 0 loop : 0.06 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 51 HIS 0.004 0.001 HIS E 114 PHE 0.011 0.001 PHE E 79 TYR 0.017 0.001 TYR B 89 ARG 0.005 0.000 ARG L 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8151 (mmm) cc_final: 0.7867 (mmm) REVERT: D 48 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9107 (tm-30) REVERT: D 112 VAL cc_start: 0.9573 (t) cc_final: 0.9320 (p) REVERT: D 116 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9219 (p) REVERT: E 51 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8537 (tp30) REVERT: G 73 ASP cc_start: 0.8911 (m-30) cc_final: 0.8652 (m-30) REVERT: G 74 ASN cc_start: 0.9149 (m-40) cc_final: 0.8819 (t0) REVERT: G 85 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8798 (tp-100) REVERT: G 95 ASN cc_start: 0.9148 (m-40) cc_final: 0.8830 (m-40) REVERT: G 105 GLN cc_start: 0.9268 (mp10) cc_final: 0.8968 (mp10) REVERT: H 114 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8482 (tp30) outliers start: 27 outliers final: 23 residues processed: 225 average time/residue: 0.2219 time to fit residues: 72.3049 Evaluate side-chains 226 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.1980 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.082643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.064355 restraints weight = 90049.967| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.11 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13035 Z= 0.202 Angle : 0.654 12.414 18661 Z= 0.366 Chirality : 0.035 0.227 2067 Planarity : 0.005 0.072 1480 Dihedral : 28.310 74.021 3881 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.88 % Allowed : 29.48 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.28), residues: 878 helix: 2.26 (0.21), residues: 637 sheet: None (None), residues: 0 loop : 0.04 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 79 HIS 0.004 0.001 HIS F 76 PHE 0.009 0.001 PHE A 68 TYR 0.011 0.001 TYR H 38 ARG 0.008 0.000 ARG L 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.53 seconds wall clock time: 44 minutes 1.80 seconds (2641.80 seconds total)