Starting phenix.real_space_refine on Wed Nov 15 15:17:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/11_2023/6yov_10864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/11_2023/6yov_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_10864/11_2023/6yov_10864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/11_2023/6yov_10864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/11_2023/6yov_10864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/11_2023/6yov_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 6.53, per 1000 atoms: 0.53 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: 6.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.46 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: 4.18 Time building geometry restraints manager: 6.82 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: 4963 17.90 - 35.81: 816 35.81 - 53.71: 816 53.71 - 71.61: 258 71.61 - 89.52: 12 Dihedral angle restraints: 6865 sinusoidal: 4395 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 6862 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 4.050 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 40.360 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.690 ------------------------------------------------------------------------------- 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 : 25.215 89.518 5315 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 *********************** 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 : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2288 time to fit residues: 114.4754 Evaluate side-chains 245 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2478 ------------------------------------------------------------------------------- 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: 5.9990 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: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 GLN F 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13035 Z= 0.286 Angle : 0.652 10.370 18661 Z= 0.375 Chirality : 0.038 0.164 2067 Planarity : 0.005 0.056 1480 Dihedral : 28.927 74.296 3645 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 5.06 % Allowed : 18.50 % Favored : 76.45 % 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: 2.57 (0.27), residues: 878 helix: 2.24 (0.20), residues: 658 sheet: None (None), residues: 0 loop : 0.09 (0.37), residues: 220 *********************** 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 311 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 276 time to evaluate : 1.022 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 outliers start: 35 outliers final: 24 residues processed: 291 average time/residue: 0.2474 time to fit residues: 101.1797 Evaluate side-chains 255 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 1.016 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.1259 time to fit residues: 6.4096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN G 25 GLN H 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13035 Z= 0.382 Angle : 0.674 11.748 18661 Z= 0.386 Chirality : 0.039 0.160 2067 Planarity : 0.005 0.046 1480 Dihedral : 29.263 74.191 3645 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.35 % Allowed : 20.95 % Favored : 73.70 % 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 (0.27), residues: 878 helix: 2.26 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.10 (0.36), residues: 230 *********************** 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 274 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 0.997 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 outliers start: 37 outliers final: 25 residues processed: 251 average time/residue: 0.2329 time to fit residues: 83.5301 Evaluate side-chains 224 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 1.035 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.1209 time to fit residues: 6.6568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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: 0.8502 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13035 Z= 0.282 Angle : 0.631 12.305 18661 Z= 0.360 Chirality : 0.037 0.146 2067 Planarity : 0.004 0.046 1480 Dihedral : 29.187 74.356 3645 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.18 % Allowed : 22.25 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.28), residues: 878 helix: 2.32 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.15 (0.37), residues: 232 *********************** 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 253 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 231 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 238 average time/residue: 0.2351 time to fit residues: 80.6755 Evaluate side-chains 224 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1078 time to fit residues: 3.7291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN C 25 GLN E 94 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13035 Z= 0.278 Angle : 0.635 11.751 18661 Z= 0.361 Chirality : 0.036 0.206 2067 Planarity : 0.005 0.052 1480 Dihedral : 29.203 74.229 3645 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.03 % Allowed : 24.86 % Favored : 72.11 % 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: 2.38 (0.28), residues: 878 helix: 2.19 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -0.17 (0.37), residues: 229 *********************** 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 251 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 238 average time/residue: 0.2426 time to fit residues: 82.4517 Evaluate side-chains 220 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1303 time to fit residues: 4.4114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13035 Z= 0.274 Angle : 0.657 16.096 18661 Z= 0.367 Chirality : 0.037 0.211 2067 Planarity : 0.004 0.059 1480 Dihedral : 29.177 74.006 3645 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.73 % Allowed : 26.45 % Favored : 71.82 % 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: 2.37 (0.28), residues: 878 helix: 2.16 (0.20), residues: 645 sheet: None (None), residues: 0 loop : -0.05 (0.37), residues: 233 *********************** 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 235 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 223 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 225 average time/residue: 0.2365 time to fit residues: 77.0795 Evaluate side-chains 207 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1126 time to fit residues: 3.0486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13035 Z= 0.200 Angle : 0.631 12.054 18661 Z= 0.355 Chirality : 0.035 0.172 2067 Planarity : 0.004 0.061 1480 Dihedral : 29.048 74.123 3645 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.01 % Allowed : 28.47 % Favored : 70.52 % 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: 2.52 (0.28), residues: 878 helix: 2.22 (0.20), residues: 643 sheet: None (None), residues: 0 loop : 0.17 (0.38), residues: 235 *********************** 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 237 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 230 time to evaluate : 1.059 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 outliers start: 7 outliers final: 2 residues processed: 232 average time/residue: 0.2388 time to fit residues: 79.7493 Evaluate side-chains 214 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 212 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1055 time to fit residues: 1.6383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 104 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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** E 94 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13035 Z= 0.314 Angle : 0.669 13.665 18661 Z= 0.377 Chirality : 0.038 0.250 2067 Planarity : 0.004 0.064 1480 Dihedral : 29.088 74.809 3645 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.75 % Allowed : 26.73 % Favored : 70.52 % 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: 2.32 (0.28), residues: 878 helix: 2.11 (0.20), residues: 643 sheet: None (None), residues: 0 loop : -0.01 (0.39), residues: 235 *********************** 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 231 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 218 average time/residue: 0.2242 time to fit residues: 70.7635 Evaluate side-chains 211 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1097 time to fit residues: 2.8362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8473 moved from start: 0.6392 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= 0.233 Angle : 0.659 13.621 18661 Z= 0.371 Chirality : 0.036 0.229 2067 Planarity : 0.004 0.057 1480 Dihedral : 29.023 74.581 3645 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.43 % Allowed : 28.76 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.28), residues: 878 helix: 1.97 (0.21), residues: 642 sheet: None (None), residues: 0 loop : 0.05 (0.39), residues: 236 *********************** 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 218 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 1.072 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 outliers start: 3 outliers final: 1 residues processed: 216 average time/residue: 0.2342 time to fit residues: 73.0465 Evaluate side-chains 207 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1101 time to fit residues: 1.4736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 40.0000 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8409 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13035 Z= 0.198 Angle : 0.654 13.157 18661 Z= 0.365 Chirality : 0.035 0.214 2067 Planarity : 0.004 0.056 1480 Dihedral : 28.891 75.393 3645 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.29 % Allowed : 28.90 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.28), residues: 878 helix: 1.96 (0.21), residues: 639 sheet: None (None), residues: 0 loop : 0.14 (0.39), residues: 239 ********************** 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 227 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 226 average time/residue: 0.2271 time to fit residues: 74.4666 Evaluate side-chains 212 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1102 time to fit residues: 1.4603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.062401 restraints weight = 90523.223| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.15 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13035 Z= 0.267 Angle : 0.668 13.914 18661 Z= 0.378 Chirality : 0.037 0.206 2067 Planarity : 0.004 0.062 1480 Dihedral : 28.895 74.767 3645 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.72 % Allowed : 30.64 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 2.22 (0.29), residues: 878 helix: 1.97 (0.21), residues: 639 sheet: None (None), residues: 0 loop : 0.22 (0.39), residues: 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.18 seconds wall clock time: 44 minutes 19.86 seconds (2659.86 seconds total)