Starting phenix.real_space_refine on Wed Mar 4 22:03:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ytf_10915/03_2026/6ytf_10915.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ytf_10915/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ytf_10915/03_2026/6ytf_10915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ytf_10915/03_2026/6ytf_10915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ytf_10915/03_2026/6ytf_10915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ytf_10915/03_2026/6ytf_10915.map" } 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-dev-5986/lib/python3.9/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: 3.74, per 1000 atoms: 0.22 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: 1.52 Conformation dependent library (CDL) restraints added in 401.2 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: 2.57 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: 4.22 Time building geometry restraints manager: 2.03 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: 25707 1.91 - 3.83: 1068 3.83 - 5.74: 95 5.74 - 7.65: 12 7.65 - 9.56: 2 Bond angle restraints: 26884 Sorted by residual: angle pdb=" C2' A 3 955 " pdb=" C1' A 3 955 " pdb=" N9 A 3 955 " ideal model delta sigma weight residual 112.00 118.03 -6.03 1.50e+00 4.44e-01 1.62e+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=" C2' A 31354 " pdb=" C1' A 31354 " pdb=" N9 A 31354 " ideal model delta sigma weight residual 112.00 116.92 -4.92 1.50e+00 4.44e-01 1.08e+01 angle pdb=" O3' U 7 27 " pdb=" C3' U 7 27 " pdb=" C2' U 7 27 " ideal model delta sigma weight residual 113.70 118.59 -4.89 1.50e+00 4.44e-01 1.06e+01 angle pdb=" C2' G 31219 " pdb=" C1' G 31219 " pdb=" N9 G 31219 " ideal model delta sigma weight residual 112.00 116.62 -4.62 1.50e+00 4.44e-01 9.47e+00 ... (remaining 26879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 10171 34.06 - 68.11: 1356 68.11 - 102.17: 147 102.17 - 136.22: 1 136.22 - 170.28: 9 Dihedral angle restraints: 11684 sinusoidal: 9248 harmonic: 2436 Sorted by residual: dihedral pdb=" O4' C 3 964 " pdb=" C1' C 3 964 " pdb=" N1 C 3 964 " pdb=" C2 C 3 964 " ideal model delta sinusoidal sigma weight residual 200.00 38.70 161.30 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" O4' C 31155 " pdb=" C1' C 31155 " pdb=" N1 C 31155 " pdb=" C2 C 31155 " ideal model delta sinusoidal sigma weight residual 200.00 49.08 150.92 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U 3 957 " pdb=" C1' U 3 957 " pdb=" N1 U 3 957 " pdb=" C2 U 3 957 " ideal model delta sinusoidal sigma weight residual 232.00 61.72 170.28 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 11681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2563 0.049 - 0.097: 651 0.097 - 0.146: 163 0.146 - 0.195: 30 0.195 - 0.244: 10 Chirality restraints: 3417 Sorted by residual: chirality pdb=" C1' U 31080 " pdb=" O4' U 31080 " pdb=" C2' U 31080 " pdb=" N1 U 31080 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' A 3 955 " pdb=" O4' A 3 955 " pdb=" C2' A 3 955 " pdb=" N9 A 3 955 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1' A 31354 " pdb=" O4' A 31354 " pdb=" C2' A 31354 " pdb=" N9 A 31354 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.35e+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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.680 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 : 0.007 0.148 18182 Z= 0.370 Angle : 0.883 9.563 26884 Z= 0.468 Chirality : 0.049 0.244 3417 Planarity : 0.007 0.162 1651 Dihedral : 23.958 170.278 10110 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 covalent geometry : bond 0.00725 (18182) covalent geometry : angle 0.88266 (26884) hydrogen bonds : bond 0.14702 ( 637) hydrogen bonds : angle 6.12778 ( 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 : 0.386 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: 0.6974 time to fit residues: 185.6325 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 : 0.370 ------------------------------------------------------------------------------- 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.180627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.166620 restraints weight = 22442.840| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 0.41 r_work: 0.3967 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18182 Z= 0.161 Angle : 0.644 7.401 26884 Z= 0.332 Chirality : 0.038 0.220 3417 Planarity : 0.005 0.052 1651 Dihedral : 23.369 170.698 8516 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 8.76 % Allowed : 33.87 % Favored : 57.37 % 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: -2.33 (0.27), residues: 836 helix: -1.61 (0.24), residues: 347 sheet: 0.22 (0.46), residues: 132 loop : -2.08 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG n 92 TYR 0.010 0.002 TYR j 5 PHE 0.019 0.002 PHE n 23 TRP 0.014 0.002 TRP d 201 HIS 0.004 0.001 HIS t 57 Details of bonding type rmsd covalent geometry : bond 0.00319 (18182) covalent geometry : angle 0.64398 (26884) hydrogen bonds : bond 0.05500 ( 637) hydrogen bonds : angle 3.96247 ( 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 232 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 31 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: d 140 ASN cc_start: 0.5352 (m-40) cc_final: 0.4911 (m110) REVERT: h 53 LYS cc_start: 0.7619 (tttm) cc_final: 0.6767 (ptpp) REVERT: h 57 ASP cc_start: 0.6054 (OUTLIER) cc_final: 0.5443 (t0) REVERT: h 70 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5727 (tpm-80) REVERT: h 123 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6449 (mm-30) REVERT: j 28 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7311 (mm) REVERT: j 105 ASP cc_start: 0.7404 (t0) cc_final: 0.6900 (t70) REVERT: n 79 ARG cc_start: 0.7102 (ttm110) cc_final: 0.6576 (ttt-90) REVERT: o 10 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5156 (tt0) REVERT: o 27 LEU cc_start: 0.8592 (mt) cc_final: 0.8264 (mt) REVERT: o 73 TYR cc_start: 0.7367 (t80) cc_final: 0.7119 (t80) REVERT: t 55 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5798 (ptp-170) outliers start: 60 outliers final: 18 residues processed: 211 average time/residue: 0.7064 time to fit residues: 163.8114 Evaluate side-chains 173 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 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 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 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: 4.9990 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 107 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 GLN h 51 GLN j 29 ASN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.180516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.157192 restraints weight = 22803.680| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 0.87 r_work: 0.3905 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18182 Z= 0.176 Angle : 0.643 7.155 26884 Z= 0.330 Chirality : 0.038 0.223 3417 Planarity : 0.005 0.048 1651 Dihedral : 23.206 170.069 8462 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 8.61 % Allowed : 34.74 % Favored : 56.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.50 (0.28), residues: 836 helix: -0.76 (0.27), residues: 346 sheet: 0.49 (0.48), residues: 137 loop : -1.78 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 204 TYR 0.012 0.002 TYR n 86 PHE 0.017 0.002 PHE h 18 TRP 0.014 0.002 TRP d 201 HIS 0.009 0.001 HIS t 69 Details of bonding type rmsd covalent geometry : bond 0.00348 (18182) covalent geometry : angle 0.64329 (26884) hydrogen bonds : bond 0.05336 ( 637) hydrogen bonds : angle 3.83928 ( 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 211 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 112 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6536 (m-30) REVERT: d 136 ARG cc_start: 0.6355 (ttm170) cc_final: 0.5678 (tpp-160) REVERT: d 140 ASN cc_start: 0.5320 (m-40) cc_final: 0.4853 (m110) REVERT: d 164 ARG cc_start: 0.6778 (mtm180) cc_final: 0.6576 (mtp85) REVERT: h 53 LYS cc_start: 0.7855 (tttm) cc_final: 0.6797 (ptpp) REVERT: h 57 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5520 (t0) REVERT: h 70 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.5468 (tpm-80) REVERT: j 28 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7448 (mm) REVERT: j 31 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7280 (ttm-80) REVERT: j 105 ASP cc_start: 0.7417 (t0) cc_final: 0.6893 (t70) REVERT: n 79 ARG cc_start: 0.7094 (ttm110) cc_final: 0.6479 (ttt-90) REVERT: o 10 GLU cc_start: 0.5547 (OUTLIER) cc_final: 0.5317 (pp20) REVERT: o 27 LEU cc_start: 0.8705 (mt) cc_final: 0.8368 (mt) REVERT: o 61 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7257 (ttt90) REVERT: o 73 TYR cc_start: 0.7394 (t80) cc_final: 0.7146 (t80) REVERT: t 55 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5761 (ptp-170) outliers start: 59 outliers final: 23 residues processed: 194 average time/residue: 0.6543 time to fit residues: 140.1358 Evaluate side-chains 176 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 161 GLU 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 41 SER Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 103 TRP Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 65 VAL 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 91 ASP 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 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: 3.9990 chunk 92 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 88 GLN h 51 GLN j 35 GLN j 79 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.176732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.160961 restraints weight = 22809.191| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 0.62 r_work: 0.3905 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18182 Z= 0.310 Angle : 0.793 10.970 26884 Z= 0.396 Chirality : 0.044 0.235 3417 Planarity : 0.006 0.051 1651 Dihedral : 23.291 170.476 8458 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 9.05 % Allowed : 34.60 % Favored : 56.35 % 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: -1.62 (0.28), residues: 836 helix: -0.86 (0.26), residues: 350 sheet: 0.27 (0.47), residues: 140 loop : -1.78 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 204 TYR 0.017 0.003 TYR t 80 PHE 0.017 0.003 PHE h 18 TRP 0.015 0.002 TRP d 201 HIS 0.006 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00618 (18182) covalent geometry : angle 0.79288 (26884) hydrogen bonds : bond 0.06901 ( 637) hydrogen bonds : angle 4.08964 ( 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 209 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 147 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 31 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6316 (tm-30) REVERT: d 154 SER cc_start: 0.8104 (t) cc_final: 0.7728 (m) REVERT: h 53 LYS cc_start: 0.7786 (tttm) cc_final: 0.6810 (ptpp) REVERT: h 57 ASP cc_start: 0.6034 (OUTLIER) cc_final: 0.5474 (t0) REVERT: h 70 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.5583 (tpm-80) REVERT: h 123 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6436 (mm-30) REVERT: j 28 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7358 (mm) REVERT: j 31 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7359 (ttm-80) REVERT: j 105 ASP cc_start: 0.7456 (t0) cc_final: 0.6924 (t70) REVERT: n 79 ARG cc_start: 0.7135 (ttm110) cc_final: 0.6580 (ttt-90) REVERT: n 107 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7092 (mmm160) REVERT: o 10 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.4332 (tp30) REVERT: o 27 LEU cc_start: 0.8578 (mt) cc_final: 0.8331 (mt) REVERT: o 61 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7458 (ttt90) REVERT: o 73 TYR cc_start: 0.7443 (t80) cc_final: 0.7202 (t80) REVERT: o 76 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6738 (tptt) REVERT: t 55 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5928 (ptp-170) outliers start: 62 outliers final: 27 residues processed: 194 average time/residue: 0.6887 time to fit residues: 146.9869 Evaluate side-chains 179 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 101 VAL 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 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 31 ARG Chi-restraints excluded: chain j residue 45 VAL 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 k residue 25 ILE Chi-restraints excluded: chain k residue 36 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 49 ILE Chi-restraints excluded: chain t residue 55 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 88 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.180361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.157244 restraints weight = 22586.019| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 0.84 r_work: 0.3913 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18182 Z= 0.167 Angle : 0.639 7.889 26884 Z= 0.327 Chirality : 0.038 0.219 3417 Planarity : 0.005 0.045 1651 Dihedral : 23.127 170.144 8458 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 7.45 % Allowed : 36.06 % Favored : 56.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.15 (0.29), residues: 836 helix: -0.43 (0.28), residues: 345 sheet: 0.43 (0.46), residues: 142 loop : -1.56 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 31 TYR 0.010 0.002 TYR t 80 PHE 0.021 0.002 PHE d 203 TRP 0.015 0.002 TRP d 201 HIS 0.003 0.001 HIS t 57 Details of bonding type rmsd covalent geometry : bond 0.00333 (18182) covalent geometry : angle 0.63869 (26884) hydrogen bonds : bond 0.05180 ( 637) hydrogen bonds : angle 3.77455 ( 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 199 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 112 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: d 136 ARG cc_start: 0.6478 (ttm170) cc_final: 0.5855 (tpp-160) REVERT: h 53 LYS cc_start: 0.7914 (tttm) cc_final: 0.6692 (ptpp) REVERT: h 57 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5537 (t0) REVERT: h 70 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5341 (tpm-80) REVERT: h 123 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6584 (mm-30) REVERT: j 28 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7433 (mm) REVERT: j 31 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7271 (ttm-80) REVERT: j 105 ASP cc_start: 0.7355 (t0) cc_final: 0.6834 (t70) REVERT: n 79 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6462 (ttt-90) REVERT: o 10 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.4968 (tt0) REVERT: o 27 LEU cc_start: 0.8725 (mt) cc_final: 0.8441 (mt) REVERT: o 73 TYR cc_start: 0.7383 (t80) cc_final: 0.7116 (t80) outliers start: 51 outliers final: 26 residues processed: 188 average time/residue: 0.6382 time to fit residues: 132.9756 Evaluate side-chains 174 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 161 GLU 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 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 31 ARG 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 25 ILE 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 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 12 ASP Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4337 r_free = 0.4337 target = 0.176091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153231 restraints weight = 22696.310| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 0.90 r_work: 0.3860 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 18182 Z= 0.329 Angle : 0.822 11.110 26884 Z= 0.409 Chirality : 0.046 0.234 3417 Planarity : 0.007 0.048 1651 Dihedral : 23.248 170.564 8451 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 9.20 % Allowed : 35.47 % Favored : 55.33 % 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: -1.51 (0.29), residues: 836 helix: -0.85 (0.27), residues: 350 sheet: 0.31 (0.47), residues: 140 loop : -1.63 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG k 31 TYR 0.016 0.003 TYR t 80 PHE 0.027 0.003 PHE d 203 TRP 0.014 0.002 TRP d 201 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00657 (18182) covalent geometry : angle 0.82199 (26884) hydrogen bonds : bond 0.07099 ( 637) hydrogen bonds : angle 4.09816 ( 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 210 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 147 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: d 136 ARG cc_start: 0.6336 (ttm170) cc_final: 0.5774 (tpm170) REVERT: h 53 LYS cc_start: 0.7954 (tttm) cc_final: 0.6702 (ptpp) REVERT: h 57 ASP cc_start: 0.6403 (OUTLIER) cc_final: 0.5461 (t0) REVERT: h 70 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.5295 (tpm-80) REVERT: h 123 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6676 (mm-30) REVERT: j 105 ASP cc_start: 0.7469 (t0) cc_final: 0.6935 (t70) REVERT: n 79 ARG cc_start: 0.7174 (ttm170) cc_final: 0.6481 (ttt-90) REVERT: n 107 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7093 (mmm160) REVERT: o 10 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.4344 (tp30) REVERT: o 61 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7479 (ttt90) REVERT: o 73 TYR cc_start: 0.7432 (t80) cc_final: 0.7184 (t80) REVERT: t 6 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7148 (ptpp) REVERT: t 55 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.6020 (ptp-170) outliers start: 63 outliers final: 31 residues processed: 194 average time/residue: 0.6683 time to fit residues: 143.0718 Evaluate side-chains 180 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 101 VAL 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 97 THR Chi-restraints excluded: chain h residue 123 GLU 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 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 91 ASP Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 66 GLU 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 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 6 LYS 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: 0.8980 chunk 87 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** n 32 ASN ** 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 = 0.4374 r_free = 0.4374 target = 0.179336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157166 restraints weight = 22543.058| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 0.80 r_work: 0.3909 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18182 Z= 0.187 Angle : 0.668 11.584 26884 Z= 0.340 Chirality : 0.039 0.219 3417 Planarity : 0.005 0.043 1651 Dihedral : 23.111 170.050 8451 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 8.18 % Allowed : 36.79 % Favored : 55.04 % 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: -1.16 (0.29), residues: 836 helix: -0.52 (0.28), residues: 344 sheet: 0.49 (0.47), residues: 140 loop : -1.47 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG k 31 TYR 0.015 0.002 TYR h 44 PHE 0.028 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 covalent geometry : bond 0.00375 (18182) covalent geometry : angle 0.66806 (26884) hydrogen bonds : bond 0.05463 ( 637) hydrogen bonds : angle 3.81809 ( 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 203 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 147 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: d 112 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6447 (m-30) REVERT: d 136 ARG cc_start: 0.6381 (ttm170) cc_final: 0.5990 (tpp-160) REVERT: h 17 LYS cc_start: 0.5407 (ttpp) cc_final: 0.5175 (pptt) REVERT: h 53 LYS cc_start: 0.7934 (tttm) cc_final: 0.6785 (ptpp) REVERT: h 57 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5467 (t0) REVERT: j 105 ASP cc_start: 0.7367 (t0) cc_final: 0.6850 (t70) REVERT: k 91 ASP cc_start: 0.3760 (OUTLIER) cc_final: 0.3492 (m-30) REVERT: n 79 ARG cc_start: 0.7151 (ttm170) cc_final: 0.6505 (ttt-90) REVERT: n 109 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6189 (mmm-85) REVERT: o 10 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.4918 (tt0) REVERT: o 27 LEU cc_start: 0.8601 (mt) cc_final: 0.8270 (mt) REVERT: o 61 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7301 (ttt90) REVERT: o 73 TYR cc_start: 0.7402 (t80) cc_final: 0.7143 (t80) REVERT: t 6 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7152 (ptpp) REVERT: t 55 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5961 (ptp-170) outliers start: 56 outliers final: 29 residues processed: 192 average time/residue: 0.6485 time to fit residues: 137.7377 Evaluate side-chains 177 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 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 97 THR 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 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 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 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 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 6 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4391 r_free = 0.4391 target = 0.180811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.166994 restraints weight = 22627.517| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 0.41 r_work: 0.3977 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18182 Z= 0.164 Angle : 0.644 11.464 26884 Z= 0.330 Chirality : 0.037 0.216 3417 Planarity : 0.005 0.042 1651 Dihedral : 23.030 170.452 8451 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 6.72 % Allowed : 39.56 % Favored : 53.72 % 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: -0.97 (0.29), residues: 836 helix: -0.32 (0.28), residues: 344 sheet: 0.59 (0.47), residues: 140 loop : -1.41 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG k 31 TYR 0.016 0.002 TYR h 44 PHE 0.012 0.002 PHE h 61 TRP 0.016 0.002 TRP d 201 HIS 0.003 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00331 (18182) covalent geometry : angle 0.64433 (26884) hydrogen bonds : bond 0.05016 ( 637) hydrogen bonds : angle 3.70403 ( 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 199 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: d 46 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6355 (tptp) REVERT: d 136 ARG cc_start: 0.6404 (ttm170) cc_final: 0.6094 (tpp-160) REVERT: d 139 GLN cc_start: 0.6601 (mt0) cc_final: 0.6360 (mt0) REVERT: h 53 LYS cc_start: 0.7740 (tttm) cc_final: 0.6726 (ptpp) REVERT: h 57 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5311 (t0) REVERT: j 105 ASP cc_start: 0.7348 (t0) cc_final: 0.6858 (t70) REVERT: k 88 MET cc_start: 0.6372 (mmt) cc_final: 0.4308 (ppp) REVERT: n 79 ARG cc_start: 0.7229 (ttm170) cc_final: 0.6549 (ttt-90) REVERT: o 10 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5750 (pp20) REVERT: o 27 LEU cc_start: 0.8501 (mt) cc_final: 0.8174 (mt) REVERT: o 61 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7224 (ttt90) REVERT: o 73 TYR cc_start: 0.7376 (t80) cc_final: 0.7118 (t80) REVERT: t 55 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5895 (ptp-170) outliers start: 46 outliers final: 26 residues processed: 189 average time/residue: 0.6459 time to fit residues: 134.9708 Evaluate side-chains 177 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain d residue 101 VAL 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 97 THR 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 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 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 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 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: 1.9990 chunk 127 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4359 r_free = 0.4359 target = 0.178111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.154707 restraints weight = 22630.058| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 0.81 r_work: 0.3883 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18182 Z= 0.242 Angle : 0.737 10.921 26884 Z= 0.372 Chirality : 0.041 0.223 3417 Planarity : 0.006 0.041 1651 Dihedral : 23.070 170.076 8450 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.72 % Allowed : 40.73 % 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: -1.20 (0.29), residues: 836 helix: -0.64 (0.27), residues: 351 sheet: 0.51 (0.48), residues: 140 loop : -1.41 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 31 TYR 0.015 0.002 TYR h 44 PHE 0.015 0.002 PHE d 130 TRP 0.013 0.002 TRP d 201 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00489 (18182) covalent geometry : angle 0.73662 (26884) hydrogen bonds : bond 0.06010 ( 637) hydrogen bonds : angle 3.86900 ( 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 189 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: d 46 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6458 (tptp) REVERT: d 51 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6286 (mmm) REVERT: d 136 ARG cc_start: 0.6609 (ttm170) cc_final: 0.6042 (tpp-160) REVERT: d 154 SER cc_start: 0.8176 (t) cc_final: 0.7767 (m) REVERT: h 35 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7697 (mttp) REVERT: h 53 LYS cc_start: 0.7764 (tttm) cc_final: 0.6613 (ptpp) REVERT: j 31 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7396 (ttm-80) REVERT: j 105 ASP cc_start: 0.7359 (t0) cc_final: 0.6838 (t70) REVERT: k 88 MET cc_start: 0.6194 (mmt) cc_final: 0.4025 (ppp) REVERT: n 79 ARG cc_start: 0.7165 (ttm170) cc_final: 0.6455 (ttt-90) REVERT: n 109 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6376 (mmm-85) REVERT: o 10 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.4987 (tt0) REVERT: o 27 LEU cc_start: 0.8722 (mt) cc_final: 0.8467 (mt) REVERT: o 61 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7345 (ttt90) REVERT: o 73 TYR cc_start: 0.7419 (t80) cc_final: 0.7144 (t80) REVERT: t 55 ARG cc_start: 0.6266 (OUTLIER) cc_final: 0.5961 (ptp-170) outliers start: 46 outliers final: 26 residues processed: 182 average time/residue: 0.6746 time to fit residues: 135.1240 Evaluate side-chains 172 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 51 MET Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 101 VAL 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 35 LYS Chi-restraints excluded: chain h residue 97 THR 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 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 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 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 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 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: 20.0000 chunk 79 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4370 r_free = 0.4370 target = 0.179020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.165099 restraints weight = 22510.567| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 0.47 r_work: 0.3958 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18182 Z= 0.216 Angle : 0.712 11.327 26884 Z= 0.361 Chirality : 0.040 0.220 3417 Planarity : 0.005 0.041 1651 Dihedral : 23.045 170.274 8450 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 6.57 % Allowed : 41.17 % Favored : 52.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.12 (0.29), residues: 836 helix: -0.62 (0.28), residues: 343 sheet: 0.51 (0.48), residues: 140 loop : -1.29 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 31 TYR 0.020 0.002 TYR h 44 PHE 0.014 0.002 PHE d 130 TRP 0.015 0.002 TRP d 201 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00437 (18182) covalent geometry : angle 0.71242 (26884) hydrogen bonds : bond 0.05655 ( 637) hydrogen bonds : angle 3.85596 ( 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 186 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 46 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6372 (tptp) REVERT: d 112 ASP cc_start: 0.6096 (OUTLIER) cc_final: 0.5701 (m-30) REVERT: d 136 ARG cc_start: 0.6648 (ttm170) cc_final: 0.6355 (tpp-160) REVERT: d 154 SER cc_start: 0.8117 (t) cc_final: 0.7742 (m) REVERT: h 35 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7702 (mttp) REVERT: h 53 LYS cc_start: 0.7702 (tttm) cc_final: 0.6724 (ptpp) REVERT: j 31 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7340 (ttm-80) REVERT: j 105 ASP cc_start: 0.7394 (t0) cc_final: 0.6887 (t70) REVERT: k 88 MET cc_start: 0.6083 (mmt) cc_final: 0.4363 (ppp) REVERT: n 79 ARG cc_start: 0.7128 (ttm170) cc_final: 0.6554 (ttt-90) REVERT: n 109 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6186 (mmm-85) REVERT: o 10 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.5051 (tt0) REVERT: o 27 LEU cc_start: 0.8538 (mt) cc_final: 0.8273 (mt) REVERT: o 61 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7316 (ttt90) REVERT: o 73 TYR cc_start: 0.7439 (t80) cc_final: 0.7169 (t80) REVERT: t 55 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5961 (ptp-170) outliers start: 45 outliers final: 30 residues processed: 178 average time/residue: 0.6191 time to fit residues: 122.2054 Evaluate side-chains 173 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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 51 GLN Chi-restraints excluded: chain h residue 63 GLU Chi-restraints excluded: chain h residue 97 THR 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 108 GLU 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 6 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4366 r_free = 0.4366 target = 0.178768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.156521 restraints weight = 22479.918| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 0.83 r_work: 0.3888 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18182 Z= 0.220 Angle : 0.727 15.114 26884 Z= 0.368 Chirality : 0.040 0.220 3417 Planarity : 0.005 0.041 1651 Dihedral : 23.041 170.155 8450 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.69 % Allowed : 42.04 % Favored : 52.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.17 (0.29), residues: 836 helix: -0.73 (0.27), residues: 345 sheet: 0.50 (0.48), residues: 140 loop : -1.24 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 31 TYR 0.027 0.002 TYR h 44 PHE 0.015 0.002 PHE d 130 TRP 0.014 0.002 TRP d 201 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd covalent geometry : bond 0.00446 (18182) covalent geometry : angle 0.72666 (26884) hydrogen bonds : bond 0.05730 ( 637) hydrogen bonds : angle 3.93355 ( 1403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5208.29 seconds wall clock time: 89 minutes 38.10 seconds (5378.10 seconds total)