Starting phenix.real_space_refine on Fri Mar 15 22:49:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t90_10406/03_2024/6t90_10406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t90_10406/03_2024/6t90_10406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t90_10406/03_2024/6t90_10406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t90_10406/03_2024/6t90_10406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t90_10406/03_2024/6t90_10406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t90_10406/03_2024/6t90_10406_updated.pdb" } resolution = 3.05 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= 0.007 sd= 0.050 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 280 5.49 5 S 22 5.16 5 C 7345 2.51 5 N 2431 2.21 5 O 2953 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 "C ASP 91": "OD1" <-> "OD2" Residue "D ARG 34": "NH1" <-> "NH2" 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 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 "G ASP 91": "OD1" <-> "OD2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13031 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} 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: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, '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: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" 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: "I" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2870 Classifications: {'DNA': 141} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 140} Chain: "J" Number of atoms: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2905 Classifications: {'DNA': 141} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 140} Chain: "K" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 593 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "L" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 636 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} 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: "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: 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: "E" 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: "G" 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 Chain: "K" 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: 6.89, per 1000 atoms: 0.53 Number of scatterers: 13031 At special positions: 0 Unit cell: (97.18, 117.82, 141.04, 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 22 16.00 P 280 15.00 O 2953 8.00 N 2431 7.00 C 7345 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 1.4 seconds 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 0 sheets defined 65.9% alpha, 0.0% beta 141 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.521A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 122 through 132 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: 3.809A 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 29 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.324A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 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 49 removed outlier: 3.517A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) 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 123 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 79 removed outlier: 3.551A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (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 26 through 29 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: 3.924A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 29 through 36 Processing helix chain 'G' and resid 48 through 73 Processing helix chain 'G' and resid 81 through 89 Processing helix chain 'G' and resid 92 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 49 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 124 removed outlier: 4.071A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 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 209 Proline residue: K 202 - end of helix Processing helix chain 'L' and resid 47 through 62 removed outlier: 3.630A 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 412 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2245 1.32 - 1.45: 5458 1.45 - 1.58: 5540 1.58 - 1.71: 547 1.71 - 1.84: 34 Bond restraints: 13824 Sorted by residual: bond pdb=" CD ARG B 93 " pdb=" NE ARG B 93 " ideal model delta sigma weight residual 1.458 1.330 0.128 1.40e-02 5.10e+03 8.37e+01 bond pdb=" CD ARG B 36 " pdb=" NE ARG B 36 " ideal model delta sigma weight residual 1.458 1.359 0.099 1.40e-02 5.10e+03 5.02e+01 bond pdb=" CD ARG B 79 " pdb=" NE ARG B 79 " ideal model delta sigma weight residual 1.458 1.360 0.098 1.40e-02 5.10e+03 4.91e+01 bond pdb=" CD ARG F 40 " pdb=" NE ARG F 40 " ideal model delta sigma weight residual 1.458 1.360 0.098 1.40e-02 5.10e+03 4.86e+01 bond pdb=" CB HIS G 83 " pdb=" CG HIS G 83 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.82e+01 ... (remaining 13819 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.49: 1094 104.49 - 112.00: 7099 112.00 - 119.52: 5233 119.52 - 127.03: 5802 127.03 - 134.54: 604 Bond angle restraints: 19832 Sorted by residual: angle pdb=" N LEU D 107 " pdb=" CA LEU D 107 " pdb=" C LEU D 107 " ideal model delta sigma weight residual 111.36 103.05 8.31 1.09e+00 8.42e-01 5.81e+01 angle pdb=" N LYS A 65 " pdb=" CA LYS A 65 " pdb=" C LYS A 65 " ideal model delta sigma weight residual 111.36 119.62 -8.26 1.09e+00 8.42e-01 5.74e+01 angle pdb=" N GLY L 54 " pdb=" CA GLY L 54 " pdb=" C GLY L 54 " ideal model delta sigma weight residual 112.49 103.43 9.06 1.21e+00 6.83e-01 5.61e+01 angle pdb=" N LYS E 65 " pdb=" CA LYS E 65 " pdb=" C LYS E 65 " ideal model delta sigma weight residual 111.36 119.51 -8.15 1.09e+00 8.42e-01 5.59e+01 angle pdb=" N LYS C 16 " pdb=" CA LYS C 16 " pdb=" C LYS C 16 " ideal model delta sigma weight residual 111.71 120.24 -8.53 1.15e+00 7.56e-01 5.50e+01 ... (remaining 19827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.28: 6426 33.28 - 66.56: 1201 66.56 - 99.84: 12 99.84 - 133.13: 0 133.13 - 166.41: 2 Dihedral angle restraints: 7641 sinusoidal: 5027 harmonic: 2614 Sorted by residual: dihedral pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " pdb=" P DA I 90 " ideal model delta sinusoidal sigma weight residual 220.00 53.59 166.41 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 4 " pdb=" C3' DG I 4 " pdb=" O3' DG I 4 " pdb=" P DA I 5 " ideal model delta sinusoidal sigma weight residual 220.00 57.11 162.89 1 3.50e+01 8.16e-04 1.53e+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 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 7638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1228 0.070 - 0.139: 713 0.139 - 0.209: 247 0.209 - 0.279: 47 0.279 - 0.349: 5 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA ASN L 68 " pdb=" N ASN L 68 " pdb=" C ASN L 68 " pdb=" CB ASN L 68 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA SER L 52 " pdb=" N SER L 52 " pdb=" C SER L 52 " pdb=" CB SER L 52 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA LYS F 32 " pdb=" N LYS F 32 " pdb=" C LYS F 32 " pdb=" CB LYS F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2237 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " 0.030 2.00e-02 2.50e+03 6.16e-02 3.80e+01 pdb=" C GLY B 103 " -0.107 2.00e-02 2.50e+03 pdb=" O GLY B 103 " 0.039 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 103 " -0.025 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C GLY F 103 " 0.086 2.00e-02 2.50e+03 pdb=" O GLY F 103 " -0.030 2.00e-02 2.50e+03 pdb=" OXT GLY F 103 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 207 " -0.047 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP K 207 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP K 207 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP K 207 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP K 207 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP K 207 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 207 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 207 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 207 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP K 207 " -0.023 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 5259 2.95 - 3.44: 11131 3.44 - 3.92: 24632 3.92 - 4.41: 29529 4.41 - 4.90: 37991 Nonbonded interactions: 108542 Sorted by model distance: nonbonded pdb=" OG1 THR F 83 " pdb=" N ALA F 84 " model vdw 2.459 2.520 nonbonded pdb=" OG1 THR B 83 " pdb=" N ALA B 84 " model vdw 2.469 2.520 nonbonded pdb=" OP1 DA J 139 " pdb=" NH2 ARG L 53 " model vdw 2.471 2.520 nonbonded pdb=" CB GLU E 98 " pdb=" OE1 GLU E 98 " model vdw 2.479 2.752 nonbonded pdb=" O ALA C 11 " pdb=" CG ARG C 12 " model vdw 2.493 3.440 ... (remaining 108537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 41 through 134 or resid 201 through 202)) } ncs_group { reference = (chain 'B' and resid 23 through 103) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 117 or resid 201)) selection = (chain 'G' and (resid 10 through 117 or resid 201)) } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.96 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: 0.920 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: 0.020 Extract box with map and model: 4.170 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 40.680 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.022 0.178 13824 Z= 1.387 Angle : 1.522 10.572 19832 Z= 1.013 Chirality : 0.093 0.349 2240 Planarity : 0.008 0.062 1530 Dihedral : 24.655 166.407 5953 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 1.02 (0.24), residues: 883 helix: 0.80 (0.18), residues: 647 sheet: None (None), residues: 0 loop : 0.72 (0.33), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.010 TRP K 207 HIS 0.008 0.002 HIS G 32 PHE 0.030 0.005 PHE L 90 TYR 0.047 0.008 TYR B 52 ARG 0.008 0.001 ARG F 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8602 (pp20) REVERT: G 39 ASN cc_start: 0.7242 (m-40) cc_final: 0.6613 (m110) REVERT: K 163 THR cc_start: 0.7350 (p) cc_final: 0.7104 (p) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3169 time to fit residues: 93.4577 Evaluate side-chains 156 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN C 74 ASN D 110 HIS G 32 HIS G 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13824 Z= 0.196 Angle : 0.602 10.936 19832 Z= 0.354 Chirality : 0.035 0.131 2240 Planarity : 0.004 0.032 1530 Dihedral : 28.377 179.369 4128 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.06 % Allowed : 6.87 % Favored : 92.07 % 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: 3.03 (0.26), residues: 883 helix: 2.51 (0.19), residues: 660 sheet: None (None), residues: 0 loop : 0.49 (0.34), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 51 HIS 0.004 0.001 HIS G 83 PHE 0.019 0.002 PHE K 187 TYR 0.016 0.001 TYR H 41 ARG 0.007 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 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: A 60 GLU cc_start: 0.7984 (pm20) cc_final: 0.7476 (pm20) REVERT: D 36 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8700 (pp20) outliers start: 8 outliers final: 3 residues processed: 224 average time/residue: 0.2938 time to fit residues: 88.7754 Evaluate side-chains 170 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain E residue 77 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 50.0000 chunk 70 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN C 39 ASN D 83 HIS D 110 HIS E 69 GLN G 74 ASN H 83 HIS H 110 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 13824 Z= 0.514 Angle : 0.671 8.898 19832 Z= 0.387 Chirality : 0.041 0.142 2240 Planarity : 0.005 0.046 1530 Dihedral : 29.281 178.649 4128 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.17 % Allowed : 9.11 % Favored : 87.71 % 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 (0.26), residues: 883 helix: 2.41 (0.19), residues: 650 sheet: None (None), residues: 0 loop : -0.36 (0.32), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 79 HIS 0.005 0.001 HIS L 101 PHE 0.020 0.002 PHE K 187 TYR 0.018 0.002 TYR H 84 ARG 0.006 0.001 ARG L 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7957 (pm20) cc_final: 0.7670 (pm20) outliers start: 24 outliers final: 15 residues processed: 182 average time/residue: 0.2871 time to fit residues: 71.8959 Evaluate side-chains 167 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN D 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13824 Z= 0.299 Angle : 0.573 10.217 19832 Z= 0.337 Chirality : 0.035 0.125 2240 Planarity : 0.004 0.044 1530 Dihedral : 28.929 173.433 4128 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.91 % Allowed : 10.83 % Favored : 86.26 % 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: 2.78 (0.27), residues: 883 helix: 2.61 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -0.55 (0.33), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 79 HIS 0.002 0.001 HIS B 76 PHE 0.027 0.002 PHE K 187 TYR 0.021 0.001 TYR H 84 ARG 0.005 0.000 ARG K 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7950 (pm20) cc_final: 0.7540 (pm20) outliers start: 22 outliers final: 15 residues processed: 170 average time/residue: 0.2642 time to fit residues: 62.8342 Evaluate side-chains 169 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN F 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 13824 Z= 0.497 Angle : 0.644 9.127 19832 Z= 0.374 Chirality : 0.040 0.140 2240 Planarity : 0.004 0.043 1530 Dihedral : 29.282 171.067 4128 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.17 % Allowed : 11.76 % Favored : 85.07 % 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: 2.41 (0.27), residues: 883 helix: 2.40 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -0.87 (0.33), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 79 HIS 0.005 0.001 HIS A 114 PHE 0.027 0.002 PHE K 187 TYR 0.019 0.002 TYR H 84 ARG 0.010 0.001 ARG L 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.151 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: A 60 GLU cc_start: 0.8001 (pm20) cc_final: 0.7632 (pm20) outliers start: 24 outliers final: 17 residues processed: 164 average time/residue: 0.2859 time to fit residues: 66.2046 Evaluate side-chains 168 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 0.0370 chunk 110 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS E 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13824 Z= 0.199 Angle : 0.542 7.681 19832 Z= 0.324 Chirality : 0.032 0.128 2240 Planarity : 0.003 0.042 1530 Dihedral : 28.751 171.396 4128 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.98 % Allowed : 12.55 % Favored : 85.47 % 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: 2.76 (0.28), residues: 883 helix: 2.69 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -0.81 (0.33), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 51 HIS 0.003 0.001 HIS B 76 PHE 0.021 0.001 PHE K 187 TYR 0.021 0.001 TYR H 84 ARG 0.005 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7825 (pm20) cc_final: 0.7539 (pm20) outliers start: 15 outliers final: 10 residues processed: 172 average time/residue: 0.2687 time to fit residues: 65.4289 Evaluate side-chains 165 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain L residue 78 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.0870 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13824 Z= 0.162 Angle : 0.542 9.763 19832 Z= 0.322 Chirality : 0.032 0.153 2240 Planarity : 0.004 0.044 1530 Dihedral : 28.689 169.153 4128 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.72 % Allowed : 13.87 % Favored : 84.41 % 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: 2.90 (0.28), residues: 883 helix: 2.74 (0.20), residues: 653 sheet: None (None), residues: 0 loop : -0.58 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 51 HIS 0.002 0.000 HIS B 76 PHE 0.026 0.002 PHE L 90 TYR 0.019 0.001 TYR H 84 ARG 0.017 0.000 ARG K 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7793 (pm20) cc_final: 0.7521 (pm20) REVERT: G 92 GLU cc_start: 0.7742 (pm20) cc_final: 0.7440 (pm20) outliers start: 13 outliers final: 12 residues processed: 175 average time/residue: 0.2563 time to fit residues: 63.6324 Evaluate side-chains 170 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 50.0000 chunk 99 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13824 Z= 0.273 Angle : 0.587 13.136 19832 Z= 0.341 Chirality : 0.034 0.124 2240 Planarity : 0.004 0.046 1530 Dihedral : 28.909 168.263 4128 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.85 % Allowed : 14.66 % Favored : 83.49 % 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: 2.81 (0.28), residues: 883 helix: 2.72 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 79 HIS 0.004 0.001 HIS B 76 PHE 0.034 0.002 PHE L 90 TYR 0.023 0.001 TYR H 84 ARG 0.005 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7810 (pm20) cc_final: 0.7515 (pm20) outliers start: 14 outliers final: 13 residues processed: 164 average time/residue: 0.2610 time to fit residues: 60.1615 Evaluate side-chains 164 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13824 Z= 0.193 Angle : 0.573 13.625 19832 Z= 0.332 Chirality : 0.033 0.182 2240 Planarity : 0.003 0.039 1530 Dihedral : 28.738 167.202 4128 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.25 % Allowed : 14.27 % Favored : 83.49 % 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: 2.86 (0.28), residues: 883 helix: 2.75 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 51 HIS 0.003 0.001 HIS B 76 PHE 0.030 0.002 PHE K 187 TYR 0.021 0.001 TYR H 84 ARG 0.005 0.000 ARG K 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7816 (pm20) cc_final: 0.7527 (pm20) outliers start: 17 outliers final: 14 residues processed: 165 average time/residue: 0.2726 time to fit residues: 63.2573 Evaluate side-chains 167 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13824 Z= 0.277 Angle : 0.604 14.158 19832 Z= 0.348 Chirality : 0.035 0.246 2240 Planarity : 0.004 0.039 1530 Dihedral : 28.991 166.790 4128 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.85 % Allowed : 15.06 % Favored : 83.09 % 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: 2.69 (0.28), residues: 883 helix: 2.61 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -0.73 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 51 HIS 0.004 0.001 HIS B 76 PHE 0.042 0.002 PHE K 187 TYR 0.021 0.002 TYR H 84 ARG 0.007 0.000 ARG L 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7811 (pm20) cc_final: 0.7517 (pm20) outliers start: 14 outliers final: 12 residues processed: 163 average time/residue: 0.2646 time to fit residues: 60.4532 Evaluate side-chains 166 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 105 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.097062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058963 restraints weight = 37044.945| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.23 r_work: 0.2783 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13824 Z= 0.228 Angle : 0.595 15.144 19832 Z= 0.343 Chirality : 0.034 0.183 2240 Planarity : 0.003 0.038 1530 Dihedral : 28.901 166.886 4128 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.59 % Allowed : 15.59 % Favored : 82.83 % 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: 2.66 (0.28), residues: 883 helix: 2.58 (0.20), residues: 651 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 51 HIS 0.004 0.001 HIS B 76 PHE 0.031 0.002 PHE K 187 TYR 0.021 0.001 TYR H 84 ARG 0.005 0.000 ARG L 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2447.80 seconds wall clock time: 44 minutes 27.96 seconds (2667.96 seconds total)