Starting phenix.real_space_refine on Sat Dec 9 20:28:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/12_2023/6yov_10864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/12_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_10864/12_2023/6yov_10864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/12_2023/6yov_10864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/12_2023/6yov_10864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/12_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-1.21rc1-5172/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: 7.10, per 1000 atoms: 0.58 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: 5.82 Conformation dependent library (CDL) restraints added in 1.3 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: 6.11 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: 4.39 Time building geometry restraints manager: 6.19 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: 0.810 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: 0.000 Extract box with map and model: 4.070 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 39.350 Find NCS groups from input model: 0.710 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- 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 : 0.887 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: 0.2212 time to fit residues: 110.9917 Evaluate side-chains 245 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2467 ------------------------------------------------------------------------------- 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: 0.8356 moved from start: 0.3427 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= 0.290 Angle : 0.653 9.782 18661 Z= 0.375 Chirality : 0.038 0.187 2067 Planarity : 0.005 0.058 1480 Dihedral : 28.416 73.834 3881 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.16 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: 2.60 (0.27), residues: 878 helix: 2.27 (0.20), residues: 658 sheet: None (None), residues: 0 loop : 0.08 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 51 HIS 0.011 0.002 HIS B 76 PHE 0.026 0.002 PHE B 62 TYR 0.023 0.002 TYR H 41 ARG 0.007 0.001 ARG L 43 *********************** 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 : 0.981 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: 35 outliers final: 22 residues processed: 290 average time/residue: 0.2385 time to fit residues: 98.0423 Evaluate side-chains 256 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 234 time to evaluate : 0.935 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.1186 time to fit residues: 5.7536 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13035 Z= 0.233 Angle : 0.605 9.813 18661 Z= 0.349 Chirality : 0.036 0.160 2067 Planarity : 0.005 0.050 1480 Dihedral : 28.446 73.593 3881 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.18 % Allowed : 21.82 % Favored : 75.00 % 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: 2.58 (0.28), residues: 878 helix: 2.32 (0.20), residues: 653 sheet: None (None), residues: 0 loop : -0.10 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 79 HIS 0.010 0.001 HIS G 32 PHE 0.015 0.002 PHE F 62 TYR 0.018 0.002 TYR B 89 ARG 0.007 0.000 ARG L 57 *********************** 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 276 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 254 time to evaluate : 1.030 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 outliers start: 22 outliers final: 11 residues processed: 260 average time/residue: 0.2363 time to fit residues: 88.5073 Evaluate side-chains 239 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1347 time to fit residues: 3.7140 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13035 Z= 0.277 Angle : 0.627 12.655 18661 Z= 0.360 Chirality : 0.037 0.183 2067 Planarity : 0.005 0.046 1480 Dihedral : 28.479 73.678 3881 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.47 % Allowed : 23.70 % 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 (0.28), residues: 878 helix: 2.29 (0.20), residues: 647 sheet: None (None), residues: 0 loop : -0.03 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP L 51 HIS 0.007 0.001 HIS B 76 PHE 0.013 0.001 PHE F 62 TYR 0.017 0.002 TYR D 43 ARG 0.004 0.000 ARG L 98 *********************** 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 262 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 244 average time/residue: 0.2363 time to fit residues: 82.8517 Evaluate side-chains 231 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1098 time to fit residues: 4.9191 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN E 94 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13035 Z= 0.419 Angle : 0.708 15.387 18661 Z= 0.401 Chirality : 0.041 0.375 2067 Planarity : 0.005 0.052 1480 Dihedral : 28.742 74.328 3881 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.03 % Allowed : 23.70 % Favored : 73.27 % 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: 2.27 (0.28), residues: 878 helix: 2.09 (0.20), residues: 639 sheet: None (None), residues: 0 loop : -0.06 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 51 HIS 0.009 0.001 HIS B 76 PHE 0.026 0.002 PHE D 71 TYR 0.014 0.002 TYR H 41 ARG 0.007 0.001 ARG H 87 *********************** 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 241 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 230 average time/residue: 0.2241 time to fit residues: 74.9143 Evaluate side-chains 210 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1081 time to fit residues: 3.3865 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13035 Z= 0.231 Angle : 0.638 11.879 18661 Z= 0.362 Chirality : 0.036 0.158 2067 Planarity : 0.004 0.052 1480 Dihedral : 28.616 74.305 3881 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.73 % Allowed : 28.03 % Favored : 70.23 % 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: 2.35 (0.28), residues: 878 helix: 2.13 (0.20), residues: 636 sheet: None (None), residues: 0 loop : 0.08 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 51 HIS 0.007 0.001 HIS B 76 PHE 0.021 0.002 PHE A 68 TYR 0.027 0.002 TYR H 41 ARG 0.005 0.000 ARG H 87 *********************** 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 240 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 1.038 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: 12 outliers final: 9 residues processed: 231 average time/residue: 0.2749 time to fit residues: 91.3145 Evaluate side-chains 215 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 206 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1078 time to fit residues: 3.0484 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** 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: 0.8462 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13035 Z= 0.215 Angle : 0.648 16.303 18661 Z= 0.362 Chirality : 0.037 0.241 2067 Planarity : 0.004 0.054 1480 Dihedral : 28.473 74.626 3881 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.87 % Allowed : 28.32 % 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: 2.37 (0.28), residues: 878 helix: 2.09 (0.20), residues: 644 sheet: None (None), residues: 0 loop : 0.18 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 51 HIS 0.007 0.001 HIS B 76 PHE 0.026 0.002 PHE D 71 TYR 0.017 0.001 TYR H 41 ARG 0.005 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 229 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 223 time to evaluate : 1.162 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: 6 outliers final: 3 residues processed: 225 average time/residue: 0.2384 time to fit residues: 76.2342 Evaluate side-chains 208 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1092 time to fit residues: 1.8280 ------------------------------------------------------------------------------- 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: 0.3980 chunk 32 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 overall best weight: 3.4984 ------------------------------------------------------------------------------- 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 H 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6276 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= 0.283 Angle : 0.667 13.256 18661 Z= 0.374 Chirality : 0.037 0.215 2067 Planarity : 0.004 0.053 1480 Dihedral : 28.494 74.674 3881 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.17 % Allowed : 27.89 % Favored : 69.94 % 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: 2.31 (0.28), residues: 878 helix: 2.04 (0.20), residues: 645 sheet: None (None), residues: 0 loop : 0.16 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 79 HIS 0.004 0.001 HIS D 110 PHE 0.011 0.002 PHE L 48 TYR 0.015 0.002 TYR H 41 ARG 0.004 0.000 ARG H 87 *********************** 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 226 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 214 average time/residue: 0.2269 time to fit residues: 70.3871 Evaluate side-chains 215 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1044 time to fit residues: 3.4223 ------------------------------------------------------------------------------- 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: 0.0000 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13035 Z= 0.203 Angle : 0.669 12.749 18661 Z= 0.374 Chirality : 0.036 0.187 2067 Planarity : 0.004 0.055 1480 Dihedral : 28.384 74.480 3881 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.29 % Allowed : 29.05 % Favored : 70.66 % 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: 2.28 (0.28), residues: 878 helix: 2.02 (0.21), residues: 643 sheet: None (None), residues: 0 loop : 0.16 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 51 HIS 0.003 0.001 HIS L 105 PHE 0.026 0.002 PHE D 71 TYR 0.013 0.001 TYR E 55 ARG 0.006 0.000 ARG L 53 *********************** 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 228 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 0.999 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: 2 outliers final: 0 residues processed: 226 average time/residue: 0.2441 time to fit residues: 78.4618 Evaluate side-chains 212 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2008 ------------------------------------------------------------------------------- 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: 40.0000 chunk 103 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 0.0370 chunk 69 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 0.4980 overall best weight: 1.6662 ------------------------------------------------------------------------------- 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: 0.8438 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13035 Z= 0.224 Angle : 0.668 13.319 18661 Z= 0.375 Chirality : 0.037 0.230 2067 Planarity : 0.004 0.053 1480 Dihedral : 28.307 74.919 3881 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.58 % Allowed : 30.35 % Favored : 69.08 % 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: 2.33 (0.28), residues: 878 helix: 2.07 (0.21), residues: 641 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 79 HIS 0.005 0.001 HIS D 110 PHE 0.012 0.001 PHE L 48 TYR 0.022 0.001 TYR E 55 ARG 0.007 0.000 ARG D 100 ********************** 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 222 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 218 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: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 219 average time/residue: 0.2599 time to fit residues: 82.2860 Evaluate side-chains 216 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1162 time to fit residues: 1.6056 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.0070 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 0.0050 overall best weight: 1.7616 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.065886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045149 restraints weight = 58044.968| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.41 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.6684 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= 0.226 Angle : 0.670 12.384 18661 Z= 0.377 Chirality : 0.037 0.275 2067 Planarity : 0.004 0.054 1480 Dihedral : 28.251 74.887 3881 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.58 % Allowed : 31.07 % Favored : 68.35 % 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: 2.32 (0.28), residues: 878 helix: 2.05 (0.21), residues: 642 sheet: None (None), residues: 0 loop : 0.19 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 79 HIS 0.006 0.001 HIS E 114 PHE 0.016 0.001 PHE L 48 TYR 0.029 0.001 TYR E 55 ARG 0.007 0.000 ARG D 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.58 seconds wall clock time: 44 minutes 13.69 seconds (2653.69 seconds total)