Starting phenix.real_space_refine on Sat Sep 12 15:41:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ytf_10915/09_2026/6ytf_10915.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ytf_10915/09_2026/6ytf_10915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ytf_10915/09_2026/6ytf_10915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ytf_10915/09_2026/6ytf_10915.map" model { file = "/net/cci-nas-00/data/ceres_data/6ytf_10915/09_2026/6ytf_10915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ytf_10915/09_2026/6ytf_10915.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ytf_10915/09_2026/6ytf_10915.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ytf_10915/09_2026/6ytf_10915.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 477 5.49 5 Mg 24 5.21 5 S 24 5.16 5 C 8747 2.51 5 N 3120 2.21 5 O 4514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16906 Number of models: 1 Model: "" Number of chains: 12 Chain: "3" Number of atoms: 9676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 9676 Classifications: {'RNAv2': 453} Modifications used: {'rna2p_pur': 35, 'rna2p_pyr': 39, 'rna3p_pur': 208, 'rna3p_pyr': 171} Link IDs: {'rna2p': 74, 'rna3p': 378} Chain breaks: 1 Chain: "7" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 428 Classifications: {'RNAv2': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "9" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Classifications: {'RNAv2': 4} Modifications used: {'rna3p_pyr': 4} Link IDs: {'rna3p': 3} Chain: "d" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1649 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "h" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "j" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "k" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 797 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "n" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "o" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 791 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 650 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "3" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 65 Unusual residues: {' MG': 23, 'T1C': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.17 Number of scatterers: 16906 At special positions: 0 Unit cell: (130.995, 138.45, 108.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 477 15.00 Mg 24 11.99 O 4514 8.00 N 3120 7.00 C 8747 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 287.4 milliseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 45.0% alpha, 17.6% beta 141 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'd' and resid 6 through 11 removed outlier: 3.509A pdb=" N ILE d 10 " --> pdb=" O HIS d 6 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 6 through 11' Processing helix chain 'd' and resid 28 through 47 removed outlier: 3.848A pdb=" N TYR d 32 " --> pdb=" O GLN d 28 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL d 39 " --> pdb=" O LYS d 35 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS d 45 " --> pdb=" O GLU d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 72 through 78 removed outlier: 3.970A pdb=" N VAL d 76 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 96 removed outlier: 4.159A pdb=" N ARG d 89 " --> pdb=" O GLU d 85 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE d 94 " --> pdb=" O GLU d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 125 Processing helix chain 'd' and resid 129 through 144 removed outlier: 3.797A pdb=" N ALA d 144 " --> pdb=" O ASN d 140 " (cutoff:3.500A) Processing helix chain 'h' and resid 20 through 31 Processing helix chain 'h' and resid 35 through 53 removed outlier: 3.849A pdb=" N GLU h 52 " --> pdb=" O GLU h 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS h 53 " --> pdb=" O ARG h 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 67 removed outlier: 3.660A pdb=" N GLU h 63 " --> pdb=" O VAL h 59 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU h 67 " --> pdb=" O GLU h 63 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 108 Processing helix chain 'h' and resid 115 through 129 removed outlier: 4.265A pdb=" N GLU h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 144 Processing helix chain 'j' and resid 32 through 37 Processing helix chain 'j' and resid 39 through 47 removed outlier: 3.532A pdb=" N ARG j 43 " --> pdb=" O ARG j 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 53 Processing helix chain 'j' and resid 69 through 89 Processing helix chain 'j' and resid 92 through 99 Processing helix chain 'k' and resid 14 through 32 removed outlier: 3.770A pdb=" N ILE k 18 " --> pdb=" O ASP k 14 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN k 20 " --> pdb=" O ARG k 16 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU k 27 " --> pdb=" O GLN k 23 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR k 28 " --> pdb=" O GLU k 24 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR k 32 " --> pdb=" O THR k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 89 Processing helix chain 'n' and resid 14 through 19 Processing helix chain 'n' and resid 20 through 22 No H-bonds generated for 'chain 'n' and resid 20 through 22' Processing helix chain 'n' and resid 26 through 37 Processing helix chain 'n' and resid 44 through 48 Processing helix chain 'n' and resid 49 through 61 removed outlier: 3.756A pdb=" N LEU n 53 " --> pdb=" O ASP n 49 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP n 54 " --> pdb=" O ASP n 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA n 55 " --> pdb=" O ALA n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 65 through 83 Processing helix chain 'n' and resid 85 through 93 Processing helix chain 'o' and resid 3 through 20 removed outlier: 3.803A pdb=" N ILE o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 33 removed outlier: 3.518A pdb=" N ALA o 32 " --> pdb=" O LYS o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 39 through 49 removed outlier: 4.221A pdb=" N MET o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 51 No H-bonds generated for 'chain 'o' and resid 50 through 51' Processing helix chain 'o' and resid 52 through 60 removed outlier: 3.753A pdb=" N SER o 56 " --> pdb=" O ARG o 53 " (cutoff:3.500A) Proline residue: o 57 - end of helix Processing helix chain 'o' and resid 80 through 90 removed outlier: 3.617A pdb=" N LEU o 84 " --> pdb=" O SER o 80 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN o 90 " --> pdb=" O ASP o 86 " (cutoff:3.500A) Processing helix chain 't' and resid 12 through 24 removed outlier: 3.612A pdb=" N ALA t 24 " --> pdb=" O GLU t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 41 through 45 Processing helix chain 't' and resid 71 through 75 Processing sheet with id=AA1, first strand: chain 'd' and resid 20 through 21 removed outlier: 6.674A pdb=" N SER d 69 " --> pdb=" O SER d 53 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE d 55 " --> pdb=" O THR d 67 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR d 67 " --> pdb=" O ILE d 55 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE d 57 " --> pdb=" O LYS d 65 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS d 65 " --> pdb=" O ILE d 57 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL d 66 " --> pdb=" O SER d 102 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASN d 104 " --> pdb=" O VAL d 66 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE d 68 " --> pdb=" O ASN d 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 165 through 171 removed outlier: 3.841A pdb=" N GLY d 148 " --> pdb=" O PHE d 203 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP d 181 " --> pdb=" O ARG d 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'j' and resid 3 through 7 removed outlier: 6.632A pdb=" N LYS j 25 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE j 63 " --> pdb=" O LYS j 25 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL j 27 " --> pdb=" O ILE j 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'k' and resid 36 through 52 removed outlier: 4.511A pdb=" N GLY k 38 " --> pdb=" O ASP k 75 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP k 75 " --> pdb=" O GLY k 38 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS k 71 " --> pdb=" O MET k 42 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR k 44 " --> pdb=" O THR k 69 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR k 69 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE k 46 " --> pdb=" O ILE k 67 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE k 67 " --> pdb=" O ILE k 46 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG k 48 " --> pdb=" O TYR k 65 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR k 65 " --> pdb=" O ARG k 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN k 50 " --> pdb=" O ASP k 63 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP k 63 " --> pdb=" O ASN k 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'k' and resid 36 through 52 removed outlier: 4.511A pdb=" N GLY k 38 " --> pdb=" O ASP k 75 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP k 75 " --> pdb=" O GLY k 38 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS k 71 " --> pdb=" O MET k 42 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR k 44 " --> pdb=" O THR k 69 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR k 69 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE k 46 " --> pdb=" O ILE k 67 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE k 67 " --> pdb=" O ILE k 46 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG k 48 " --> pdb=" O TYR k 65 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR k 65 " --> pdb=" O ARG k 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN k 50 " --> pdb=" O ASP k 63 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP k 63 " --> pdb=" O ASN k 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 't' and resid 31 through 33 282 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 596 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2429 1.33 - 1.45: 7222 1.45 - 1.57: 7536 1.57 - 1.69: 950 1.69 - 1.82: 45 Bond restraints: 18182 Sorted by residual: bond pdb=" C21 T1C 31624 " pdb=" N21 T1C 31624 " ideal model delta sigma weight residual 1.326 1.474 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" C THR k 53 " pdb=" N SER k 54 " ideal model delta sigma weight residual 1.329 1.209 0.120 3.03e-02 1.09e+03 1.57e+01 bond pdb=" C21 T1C 31624 " pdb=" O21 T1C 31624 " ideal model delta sigma weight residual 1.261 1.217 0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C LYS j 121 " pdb=" N ARG j 122 " ideal model delta sigma weight residual 1.327 1.292 0.035 1.71e-02 3.42e+03 4.11e+00 bond pdb=" C1 T1C 31624 " pdb=" C2 T1C 31624 " ideal model delta sigma weight residual 1.452 1.413 0.039 2.00e-02 2.50e+03 3.75e+00 ... (remaining 18177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 24632 1.91 - 3.83: 1808 3.83 - 5.74: 403 5.74 - 7.65: 35 7.65 - 9.56: 6 Bond angle restraints: 26884 Sorted by residual: angle pdb=" O3' G 31050 " pdb=" C3' G 31050 " pdb=" C2' G 31050 " ideal model delta sigma weight residual 113.80 104.90 8.90 2.00e+00 2.50e-01 1.98e+01 angle pdb=" C3' U 7 27 " pdb=" O3' U 7 27 " pdb=" P C 7 28 " ideal model delta sigma weight residual 119.70 124.27 -4.57 1.20e+00 6.94e-01 1.45e+01 angle pdb=" O3' A 31064 " pdb=" C3' A 31064 " pdb=" C2' A 31064 " ideal model delta sigma weight residual 113.80 106.89 6.91 2.00e+00 2.50e-01 1.20e+01 angle pdb=" N GLY d 13 " pdb=" CA GLY d 13 " pdb=" C GLY d 13 " ideal model delta sigma weight residual 115.62 109.96 5.66 1.71e+00 3.42e-01 1.09e+01 angle pdb=" O3' G 31344 " pdb=" C3' G 31344 " pdb=" C2' G 31344 " ideal model delta sigma weight residual 113.80 107.34 6.46 2.00e+00 2.50e-01 1.04e+01 ... (remaining 26879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.13: 8017 23.13 - 46.26: 1270 46.26 - 69.39: 610 69.39 - 92.52: 78 92.52 - 115.65: 1 Dihedral angle restraints: 9976 sinusoidal: 7540 harmonic: 2436 Sorted by residual: dihedral pdb=" C4' G 31050 " pdb=" C3' G 31050 " pdb=" C2' G 31050 " pdb=" C1' G 31050 " ideal model delta sinusoidal sigma weight residual 36.35 -42.87 79.21 1 3.10e+00 1.04e-01 8.12e+02 dihedral pdb=" C4' G 31187 " pdb=" C3' G 31187 " pdb=" C2' G 31187 " pdb=" C1' G 31187 " ideal model delta sinusoidal sigma weight residual 36.34 -41.78 78.13 1 3.10e+00 1.04e-01 7.93e+02 dihedral pdb=" C4' C 31211 " pdb=" C3' C 31211 " pdb=" C2' C 31211 " pdb=" C1' C 31211 " ideal model delta sinusoidal sigma weight residual 36.34 -41.63 77.97 1 3.10e+00 1.04e-01 7.91e+02 ... (remaining 9973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2431 0.074 - 0.149: 361 0.149 - 0.223: 308 0.223 - 0.298: 298 0.298 - 0.372: 19 Chirality restraints: 3417 Sorted by residual: chirality pdb=" C3' G 31050 " pdb=" C4' G 31050 " pdb=" O3' G 31050 " pdb=" C2' G 31050 " both_signs ideal model delta sigma weight residual False -2.50 -2.87 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C3' G 31187 " pdb=" C4' G 31187 " pdb=" O3' G 31187 " pdb=" C2' G 31187 " both_signs ideal model delta sigma weight residual False -2.50 -2.85 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C2' G 31172 " pdb=" C3' G 31172 " pdb=" O2' G 31172 " pdb=" C1' G 31172 " both_signs ideal model delta sigma weight residual False -2.79 -2.45 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3414 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C9 T1C 31624 " -0.194 2.00e-02 2.50e+03 1.62e-01 3.28e+02 pdb=" C91 T1C 31624 " 0.054 2.00e-02 2.50e+03 pdb=" C92 T1C 31624 " -0.132 2.00e-02 2.50e+03 pdb=" N9 T1C 31624 " 0.271 2.00e-02 2.50e+03 pdb=" O91 T1C 31624 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 3 955 " -0.052 2.00e-02 2.50e+03 2.36e-02 1.53e+01 pdb=" N9 A 3 955 " 0.053 2.00e-02 2.50e+03 pdb=" C8 A 3 955 " 0.009 2.00e-02 2.50e+03 pdb=" N7 A 3 955 " -0.006 2.00e-02 2.50e+03 pdb=" C5 A 3 955 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 3 955 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A 3 955 " -0.012 2.00e-02 2.50e+03 pdb=" N1 A 3 955 " -0.009 2.00e-02 2.50e+03 pdb=" C2 A 3 955 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A 3 955 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 3 955 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 31219 " -0.047 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" N9 G 31219 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G 31219 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G 31219 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G 31219 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 31219 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G 31219 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 31219 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G 31219 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 31219 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G 31219 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G 31219 " -0.001 2.00e-02 2.50e+03 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 151 2.50 - 3.10: 11454 3.10 - 3.70: 31811 3.70 - 4.30: 46895 4.30 - 4.90: 64206 Nonbonded interactions: 154517 Sorted by model distance: nonbonded pdb=" OP1 G 31091 " pdb="MG MG 31616 " model vdw 1.898 2.170 nonbonded pdb=" OP2 G 31091 " pdb="MG MG 31616 " model vdw 1.909 2.170 nonbonded pdb=" O6 G 31105 " pdb="MG MG 31608 " model vdw 1.953 2.170 nonbonded pdb=" OP1 C 3 977 " pdb="MG MG 31613 " model vdw 1.973 2.170 nonbonded pdb=" OP2 U 31092 " pdb="MG MG 31608 " model vdw 1.983 2.170 ... (remaining 154512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.680 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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 : 0.008 0.148 18182 Z= 0.368 Angle : 1.141 9.563 26884 Z= 0.499 Chirality : 0.109 0.372 3417 Planarity : 0.007 0.162 1651 Dihedral : 22.588 115.650 8402 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.73 % Favored : 91.03 % Rotamer: Outliers : 11.09 % Allowed : 32.12 % Favored : 56.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.24), residues: 836 helix: -3.22 (0.19), residues: 344 sheet: -0.70 (0.44), residues: 133 loop : -2.89 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG j 122 TYR 0.017 0.003 TYR t 80 PHE 0.023 0.003 PHE n 23 TRP 0.027 0.003 TRP d 22 HIS 0.007 0.002 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.37 (18182) covalent geometry : angle 1.14126 / 0.50 (26884) hydrogen bonds : bond 0.14702 / 7.60 ( 637) hydrogen bonds : angle 6.12778 / 2.44 ( 1403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 182 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 58 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6184 (mt-10) REVERT: h 53 LYS cc_start: 0.7225 (tttm) cc_final: 0.6802 (ptpp) REVERT: k 14 ASP cc_start: 0.5082 (t70) cc_final: 0.4198 (t70) REVERT: k 85 ASP cc_start: 0.3669 (OUTLIER) cc_final: 0.3431 (p0) REVERT: n 76 ASN cc_start: 0.6346 (OUTLIER) cc_final: 0.5286 (m-40) REVERT: n 79 ARG cc_start: 0.6974 (ttm110) cc_final: 0.6616 (ttt-90) REVERT: o 73 TYR cc_start: 0.7373 (t80) cc_final: 0.7119 (t80) REVERT: t 35 SER cc_start: 0.6216 (OUTLIER) cc_final: 0.5988 (t) outliers start: 76 outliers final: 35 residues processed: 242 average time/residue: 0.6028 time to fit residues: 161.7865 Evaluate side-chains 192 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 153 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 66 LYS Chi-restraints excluded: chain j residue 97 ARG Chi-restraints excluded: chain j residue 98 GLN Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 45 ILE Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 76 ASN Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 35 SER Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 50 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 3 GLN d 6 HIS d 21 ASN d 28 GLN d 88 GLN d 93 ASN d 140 ASN h 21 GLN h 51 GLN j 29 ASN j 73 GLN j 79 HIS k 35 GLN k 58 ASN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 71 HIS t 14 HIS ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.184045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.170055 restraints weight = 22613.049| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 0.39 r_work: 0.4009 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18182 Z= 0.251 Angle : 1.400 21.886 26884 Z= 0.555 Chirality : 0.122 1.294 3417 Planarity : 0.006 0.052 1651 Dihedral : 19.116 164.799 6808 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 9.20 % Allowed : 33.87 % Favored : 56.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.27), residues: 836 helix: -1.65 (0.24), residues: 345 sheet: 0.18 (0.46), residues: 132 loop : -2.12 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG n 109 TYR 0.012 0.002 TYR j 5 PHE 0.019 0.002 PHE n 23 TRP 0.015 0.002 TRP d 201 HIS 0.004 0.001 HIS d 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.25 (18182) covalent geometry : angle 1.39961 / 0.56 (26884) hydrogen bonds : bond 0.07085 / 3.73 ( 637) hydrogen bonds : angle 4.04390 / 1.64 ( 1403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 31 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6497 (tm-30) REVERT: d 140 ASN cc_start: 0.5409 (m-40) cc_final: 0.5017 (m110) REVERT: h 53 LYS cc_start: 0.7630 (tttm) cc_final: 0.6805 (ptpp) REVERT: h 57 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5427 (t0) REVERT: h 70 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.5749 (tpm-80) REVERT: h 123 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6396 (mm-30) REVERT: j 28 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7337 (mm) REVERT: j 105 ASP cc_start: 0.7434 (t0) cc_final: 0.6900 (t70) REVERT: n 79 ARG cc_start: 0.7063 (ttm110) cc_final: 0.6635 (ttt-90) REVERT: o 10 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.5214 (tt0) REVERT: o 27 LEU cc_start: 0.8546 (mt) cc_final: 0.8206 (mt) REVERT: o 73 TYR cc_start: 0.7391 (t80) cc_final: 0.7128 (t80) REVERT: t 55 ARG cc_start: 0.6237 (OUTLIER) cc_final: 0.5887 (ptp-170) outliers start: 63 outliers final: 22 residues processed: 214 average time/residue: 0.5900 time to fit residues: 139.9663 Evaluate side-chains 179 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 31 GLU Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 161 GLU Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 123 GLU Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 108 GLU Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 26 ASN Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 69 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 107 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 28 GLN d 88 GLN h 51 GLN j 29 ASN j 35 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.182506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.161225 restraints weight = 22910.734| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 0.85 r_work: 0.3961 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18182 Z= 0.247 Angle : 1.262 17.879 26884 Z= 0.508 Chirality : 0.105 0.844 3417 Planarity : 0.006 0.049 1651 Dihedral : 18.940 178.146 6756 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.42 % Favored : 92.46 % Rotamer: Outliers : 9.78 % Allowed : 33.43 % Favored : 56.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.28), residues: 836 helix: -0.96 (0.26), residues: 351 sheet: 0.33 (0.47), residues: 140 loop : -1.82 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG n 109 TYR 0.011 0.002 TYR t 80 PHE 0.017 0.002 PHE n 23 TRP 0.015 0.002 TRP d 201 HIS 0.016 0.002 HIS t 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.25 (18182) covalent geometry : angle 1.26163 / 0.51 (26884) hydrogen bonds : bond 0.06650 / 3.46 ( 637) hydrogen bonds : angle 3.93958 / 1.62 ( 1403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 153 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 112 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6555 (m-30) REVERT: d 211 MET cc_start: 0.5142 (mtt) cc_final: 0.4938 (mtp) REVERT: h 53 LYS cc_start: 0.7889 (tttm) cc_final: 0.6838 (ptpp) REVERT: h 57 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.5494 (t0) REVERT: h 70 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.5581 (tpm-80) REVERT: j 28 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7423 (mm) REVERT: j 31 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7204 (ttm-80) REVERT: j 105 ASP cc_start: 0.7407 (t0) cc_final: 0.6868 (t70) REVERT: n 75 MET cc_start: 0.5732 (OUTLIER) cc_final: 0.5459 (ttp) REVERT: n 79 ARG cc_start: 0.7083 (ttm110) cc_final: 0.6526 (ttt-90) REVERT: o 10 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.5042 (tt0) REVERT: o 27 LEU cc_start: 0.8685 (mt) cc_final: 0.8334 (mt) REVERT: o 61 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7331 (ttt90) REVERT: o 73 TYR cc_start: 0.7411 (t80) cc_final: 0.7127 (t80) REVERT: t 55 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.5972 (ptp-170) outliers start: 67 outliers final: 26 residues processed: 197 average time/residue: 0.6086 time to fit residues: 132.9719 Evaluate side-chains 178 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 184 TYR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 88 GLN h 51 GLN j 35 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.178474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157179 restraints weight = 22863.594| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 0.87 r_work: 0.3896 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 18182 Z= 0.374 Angle : 1.430 24.063 26884 Z= 0.575 Chirality : 0.116 0.961 3417 Planarity : 0.007 0.052 1651 Dihedral : 18.993 177.430 6751 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.85 % Favored : 91.03 % Rotamer: Outliers : 9.64 % Allowed : 34.74 % Favored : 55.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.28), residues: 836 helix: -1.07 (0.26), residues: 349 sheet: 0.18 (0.47), residues: 140 loop : -1.78 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG h 4 TYR 0.016 0.003 TYR t 80 PHE 0.019 0.003 PHE d 130 TRP 0.016 0.003 TRP d 201 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.37 (18182) covalent geometry : angle 1.43027 / 0.57 (26884) hydrogen bonds : bond 0.07574 / 3.98 ( 637) hydrogen bonds : angle 4.21938 / 1.74 ( 1403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 31 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: d 211 MET cc_start: 0.5123 (mtt) cc_final: 0.4768 (mtp) REVERT: h 3 ARG cc_start: 0.5627 (mmm160) cc_final: 0.5407 (mmm160) REVERT: h 53 LYS cc_start: 0.7903 (tttm) cc_final: 0.6731 (ptpp) REVERT: h 57 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.5465 (t0) REVERT: h 70 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.5394 (tpm-80) REVERT: h 123 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: j 28 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7509 (mm) REVERT: j 31 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7377 (ttm-80) REVERT: j 105 ASP cc_start: 0.7431 (t0) cc_final: 0.6849 (t70) REVERT: j 107 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8079 (mtm180) REVERT: j 127 LYS cc_start: 0.5741 (OUTLIER) cc_final: 0.4793 (tttm) REVERT: n 75 MET cc_start: 0.5962 (tmm) cc_final: 0.5688 (tmt) REVERT: n 79 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6384 (ttt-90) REVERT: n 107 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7097 (mmm160) REVERT: o 10 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.4381 (tp30) REVERT: o 46 LEU cc_start: 0.8234 (pp) cc_final: 0.7825 (mt) REVERT: o 61 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7472 (ttt90) REVERT: o 73 TYR cc_start: 0.7453 (t80) cc_final: 0.7188 (t80) REVERT: o 76 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6577 (tptt) REVERT: t 20 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.5071 (pp20) outliers start: 66 outliers final: 36 residues processed: 194 average time/residue: 0.6073 time to fit residues: 130.1374 Evaluate side-chains 186 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 31 GLU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 184 TYR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain h residue 103 TRP Chi-restraints excluded: chain h residue 123 GLU Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 107 ARG Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain j residue 127 LYS Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 107 ARG Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 55 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 88 GLN h 51 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.182988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.169944 restraints weight = 22749.445| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 0.37 r_work: 0.4021 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18182 Z= 0.231 Angle : 1.203 18.891 26884 Z= 0.486 Chirality : 0.098 0.812 3417 Planarity : 0.006 0.050 1651 Dihedral : 18.693 178.280 6751 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 9.64 % Allowed : 34.45 % Favored : 55.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.29), residues: 836 helix: -0.67 (0.27), residues: 349 sheet: 0.35 (0.47), residues: 140 loop : -1.58 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 31 TYR 0.012 0.002 TYR t 80 PHE 0.014 0.002 PHE n 23 TRP 0.016 0.002 TRP d 201 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (18182) covalent geometry : angle 1.20320 / 0.49 (26884) hydrogen bonds : bond 0.06234 / 3.26 ( 637) hydrogen bonds : angle 3.85875 / 1.60 ( 1403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 150 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: d 112 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6306 (m-30) REVERT: d 211 MET cc_start: 0.5492 (mtt) cc_final: 0.5200 (mtp) REVERT: h 53 LYS cc_start: 0.7810 (tttm) cc_final: 0.6882 (ptpp) REVERT: h 57 ASP cc_start: 0.6075 (OUTLIER) cc_final: 0.5521 (t0) REVERT: h 70 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5538 (tpm-80) REVERT: h 123 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6390 (mm-30) REVERT: j 31 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7301 (ttm-80) REVERT: j 105 ASP cc_start: 0.7405 (t0) cc_final: 0.6871 (t70) REVERT: j 107 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8099 (mtm180) REVERT: n 75 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.6024 (tmt) REVERT: n 79 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6571 (ttt-90) REVERT: n 109 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6251 (mmm-85) REVERT: o 10 GLU cc_start: 0.5631 (OUTLIER) cc_final: 0.5048 (tt0) REVERT: o 27 LEU cc_start: 0.8521 (mt) cc_final: 0.8197 (mt) REVERT: o 46 LEU cc_start: 0.8219 (pp) cc_final: 0.7865 (mt) REVERT: o 73 TYR cc_start: 0.7369 (t80) cc_final: 0.7090 (t80) REVERT: o 76 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6419 (tptt) REVERT: t 20 GLU cc_start: 0.5138 (OUTLIER) cc_final: 0.4821 (pp20) REVERT: t 55 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5886 (ptp-170) outliers start: 66 outliers final: 29 residues processed: 202 average time/residue: 0.6128 time to fit residues: 136.9926 Evaluate side-chains 183 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 123 GLU Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 107 ARG Chi-restraints excluded: chain j residue 108 GLU Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 109 ARG Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 88 GLN h 51 GLN j 98 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.178647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.157736 restraints weight = 22835.912| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 0.78 r_work: 0.3910 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 18182 Z= 0.367 Angle : 1.405 22.677 26884 Z= 0.567 Chirality : 0.112 0.917 3417 Planarity : 0.007 0.049 1651 Dihedral : 18.846 178.285 6751 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.25 % Favored : 91.63 % Rotamer: Outliers : 9.78 % Allowed : 35.62 % Favored : 54.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.28), residues: 836 helix: -1.01 (0.26), residues: 350 sheet: 0.17 (0.46), residues: 140 loop : -1.65 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG k 31 TYR 0.015 0.003 TYR t 80 PHE 0.020 0.003 PHE d 130 TRP 0.016 0.002 TRP d 201 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.37 (18182) covalent geometry : angle 1.40456 / 0.57 (26884) hydrogen bonds : bond 0.07469 / 3.93 ( 637) hydrogen bonds : angle 4.12354 / 1.70 ( 1403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 145 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: d 46 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6429 (tptp) REVERT: d 211 MET cc_start: 0.5213 (mtt) cc_final: 0.4821 (mtp) REVERT: h 35 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7687 (mttp) REVERT: h 53 LYS cc_start: 0.7881 (tttm) cc_final: 0.6676 (ptpp) REVERT: h 70 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.5241 (tpm-80) REVERT: h 123 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: j 105 ASP cc_start: 0.7385 (t0) cc_final: 0.6813 (t70) REVERT: j 107 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8116 (mtm180) REVERT: n 75 MET cc_start: 0.5993 (tmm) cc_final: 0.5729 (tmt) REVERT: n 79 ARG cc_start: 0.7206 (ttm170) cc_final: 0.6478 (ttt-90) REVERT: n 107 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7098 (mmm160) REVERT: n 109 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6612 (mmm-85) REVERT: o 10 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.4358 (tp30) REVERT: o 27 LEU cc_start: 0.8684 (mt) cc_final: 0.8291 (mt) REVERT: o 46 LEU cc_start: 0.8253 (pp) cc_final: 0.7849 (mt) REVERT: o 61 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7449 (ttt90) REVERT: o 73 TYR cc_start: 0.7422 (t80) cc_final: 0.7155 (t80) REVERT: o 76 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6468 (tptt) outliers start: 67 outliers final: 37 residues processed: 197 average time/residue: 0.6027 time to fit residues: 131.6708 Evaluate side-chains 185 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 46 LYS Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 184 TYR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 123 GLU Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 107 ARG Chi-restraints excluded: chain j residue 108 GLU Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 107 ARG Chi-restraints excluded: chain n residue 109 ARG Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 0.0060 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 51 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.185950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.165211 restraints weight = 22603.456| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 0.78 r_work: 0.4026 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18182 Z= 0.173 Angle : 1.125 17.385 26884 Z= 0.456 Chirality : 0.091 0.778 3417 Planarity : 0.005 0.048 1651 Dihedral : 18.537 179.772 6751 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 7.59 % Allowed : 38.10 % Favored : 54.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.29), residues: 836 helix: -0.45 (0.27), residues: 345 sheet: 0.50 (0.47), residues: 140 loop : -1.41 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 31 TYR 0.009 0.002 TYR d 23 PHE 0.011 0.001 PHE n 23 TRP 0.017 0.002 TRP d 201 HIS 0.003 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (18182) covalent geometry : angle 1.12504 / 0.46 (26884) hydrogen bonds : bond 0.05789 / 3.02 ( 637) hydrogen bonds : angle 3.69218 / 1.53 ( 1403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: d 211 MET cc_start: 0.5361 (mtt) cc_final: 0.5100 (mtp) REVERT: h 53 LYS cc_start: 0.7877 (tttm) cc_final: 0.6801 (ptpp) REVERT: h 57 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5192 (t0) REVERT: h 70 ARG cc_start: 0.5536 (OUTLIER) cc_final: 0.5317 (tpm-80) REVERT: j 105 ASP cc_start: 0.7327 (t0) cc_final: 0.6797 (t70) REVERT: k 88 MET cc_start: 0.6269 (mmt) cc_final: 0.4203 (ppp) REVERT: n 75 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5928 (ttp) REVERT: n 79 ARG cc_start: 0.7163 (ttm170) cc_final: 0.6472 (ttt-90) REVERT: o 10 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5323 (tt0) REVERT: o 27 LEU cc_start: 0.8585 (mt) cc_final: 0.8214 (mt) REVERT: o 46 LEU cc_start: 0.8262 (pp) cc_final: 0.7860 (mt) REVERT: o 73 TYR cc_start: 0.7345 (t80) cc_final: 0.7074 (t80) outliers start: 52 outliers final: 24 residues processed: 193 average time/residue: 0.6466 time to fit residues: 138.5644 Evaluate side-chains 171 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 184 TYR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 66 GLU Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 51 GLN j 98 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.182583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.160605 restraints weight = 22736.802| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 0.80 r_work: 0.3977 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18182 Z= 0.239 Angle : 1.201 19.315 26884 Z= 0.488 Chirality : 0.096 0.827 3417 Planarity : 0.006 0.046 1651 Dihedral : 18.554 177.628 6747 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.42 % Allowed : 41.02 % Favored : 52.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.29), residues: 836 helix: -0.61 (0.27), residues: 351 sheet: 0.64 (0.47), residues: 140 loop : -1.38 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 31 TYR 0.018 0.002 TYR h 44 PHE 0.015 0.002 PHE d 130 TRP 0.014 0.002 TRP d 201 HIS 0.003 0.001 HIS d 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 (18182) covalent geometry : angle 1.20124 / 0.49 (26884) hydrogen bonds : bond 0.06213 / 3.27 ( 637) hydrogen bonds : angle 3.76866 / 1.57 ( 1403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: d 112 ASP cc_start: 0.6220 (OUTLIER) cc_final: 0.5827 (m-30) REVERT: d 211 MET cc_start: 0.5426 (mtt) cc_final: 0.5166 (mtp) REVERT: h 35 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7718 (mttp) REVERT: h 53 LYS cc_start: 0.7714 (tttm) cc_final: 0.6595 (ptpp) REVERT: j 105 ASP cc_start: 0.7310 (t0) cc_final: 0.6786 (t70) REVERT: k 88 MET cc_start: 0.6137 (mmt) cc_final: 0.4142 (ppp) REVERT: n 75 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5828 (ttp) REVERT: n 79 ARG cc_start: 0.7192 (ttm170) cc_final: 0.6481 (ttt-90) REVERT: o 10 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5217 (tt0) REVERT: o 27 LEU cc_start: 0.8669 (mt) cc_final: 0.8292 (mt) REVERT: o 46 LEU cc_start: 0.8262 (pp) cc_final: 0.7980 (mm) REVERT: o 61 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7276 (ttt90) REVERT: o 73 TYR cc_start: 0.7401 (t80) cc_final: 0.7124 (t80) REVERT: o 76 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6326 (tptt) outliers start: 44 outliers final: 23 residues processed: 180 average time/residue: 0.6543 time to fit residues: 130.5410 Evaluate side-chains 170 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 108 GLU Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 66 GLU Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 51 GLN j 98 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.181596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.167351 restraints weight = 22689.545| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 0.41 r_work: 0.3991 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18182 Z= 0.267 Angle : 1.251 20.301 26884 Z= 0.510 Chirality : 0.099 0.836 3417 Planarity : 0.006 0.045 1651 Dihedral : 18.624 178.151 6746 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.84 % Allowed : 42.77 % Favored : 51.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.29), residues: 836 helix: -0.79 (0.27), residues: 350 sheet: 0.62 (0.48), residues: 140 loop : -1.36 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG k 31 TYR 0.022 0.003 TYR h 44 PHE 0.016 0.002 PHE d 130 TRP 0.014 0.002 TRP d 201 HIS 0.003 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.27 (18182) covalent geometry : angle 1.25074 / 0.51 (26884) hydrogen bonds : bond 0.06481 / 3.41 ( 637) hydrogen bonds : angle 3.89370 / 1.61 ( 1403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 211 MET cc_start: 0.5385 (mtt) cc_final: 0.5087 (mtp) REVERT: h 35 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7717 (mttp) REVERT: h 53 LYS cc_start: 0.7620 (tttm) cc_final: 0.6676 (ptpp) REVERT: j 105 ASP cc_start: 0.7375 (t0) cc_final: 0.6863 (t70) REVERT: k 88 MET cc_start: 0.6169 (mmt) cc_final: 0.4387 (ppp) REVERT: n 75 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5956 (tmt) REVERT: n 79 ARG cc_start: 0.7170 (ttm170) cc_final: 0.6598 (ttt-90) REVERT: o 10 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5075 (tt0) REVERT: o 46 LEU cc_start: 0.8247 (pp) cc_final: 0.8016 (mm) REVERT: o 61 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7308 (ttt90) REVERT: o 73 TYR cc_start: 0.7426 (t80) cc_final: 0.7152 (t80) REVERT: o 76 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6337 (tptt) outliers start: 40 outliers final: 26 residues processed: 173 average time/residue: 0.6436 time to fit residues: 123.4880 Evaluate side-chains 170 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain h residue 51 GLN Chi-restraints excluded: chain h residue 63 GLU Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 108 GLU Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 78 optimal weight: 0.0980 chunk 79 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 51 GLN j 98 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN o 90 GLN ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.187963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.167607 restraints weight = 22571.411| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 0.78 r_work: 0.4043 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18182 Z= 0.163 Angle : 1.091 16.559 26884 Z= 0.447 Chirality : 0.087 0.760 3417 Planarity : 0.005 0.046 1651 Dihedral : 18.426 179.822 6746 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.23 % Allowed : 44.67 % Favored : 51.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.30), residues: 836 helix: -0.47 (0.28), residues: 343 sheet: 0.79 (0.47), residues: 140 loop : -1.14 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG h 49 TYR 0.021 0.002 TYR h 44 PHE 0.011 0.001 PHE n 23 TRP 0.018 0.002 TRP d 201 HIS 0.003 0.001 HIS t 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (18182) covalent geometry : angle 1.09078 / 0.45 (26884) hydrogen bonds : bond 0.05743 / 2.99 ( 637) hydrogen bonds : angle 3.72615 / 1.54 ( 1403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: h 35 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7563 (mttp) REVERT: h 51 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6551 (pp30) REVERT: h 53 LYS cc_start: 0.7672 (tttm) cc_final: 0.6734 (ptpp) REVERT: j 93 LYS cc_start: 0.7309 (tttt) cc_final: 0.7080 (tttt) REVERT: j 105 ASP cc_start: 0.7242 (t0) cc_final: 0.6722 (t70) REVERT: k 88 MET cc_start: 0.6184 (mmt) cc_final: 0.4298 (ppp) REVERT: n 75 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5779 (ttp) REVERT: n 79 ARG cc_start: 0.7082 (ttm170) cc_final: 0.6371 (ttt-90) REVERT: o 10 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5252 (tt0) REVERT: o 27 LEU cc_start: 0.8663 (mt) cc_final: 0.8404 (mt) REVERT: o 46 LEU cc_start: 0.8334 (pp) cc_final: 0.8076 (mm) REVERT: o 61 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7084 (ttt90) REVERT: o 73 TYR cc_start: 0.7317 (t80) cc_final: 0.7045 (t80) outliers start: 29 outliers final: 17 residues processed: 170 average time/residue: 0.6099 time to fit residues: 115.5286 Evaluate side-chains 163 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain h residue 51 GLN Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain t residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 0.0570 chunk 78 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 51 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.185216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.164323 restraints weight = 22513.700| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 0.77 r_work: 0.4004 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18182 Z= 0.214 Angle : 1.142 18.180 26884 Z= 0.468 Chirality : 0.090 0.781 3417 Planarity : 0.005 0.059 1651 Dihedral : 18.412 178.253 6744 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.65 % Allowed : 45.84 % Favored : 50.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.30), residues: 836 helix: -0.58 (0.28), residues: 346 sheet: 0.81 (0.48), residues: 140 loop : -1.13 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG h 3 TYR 0.020 0.002 TYR h 44 PHE 0.018 0.002 PHE d 203 TRP 0.015 0.002 TRP d 201 HIS 0.003 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (18182) covalent geometry : angle 1.14154 / 0.47 (26884) hydrogen bonds : bond 0.05887 / 3.09 ( 637) hydrogen bonds : angle 3.77604 / 1.56 ( 1403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.69 seconds wall clock time: 87 minutes 33.25 seconds (5253.25 seconds total)