Starting phenix.real_space_refine on Wed Aug 7 04:23:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/08_2024/7afk_11768_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/08_2024/7afk_11768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/08_2024/7afk_11768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/08_2024/7afk_11768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/08_2024/7afk_11768_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/08_2024/7afk_11768_neut.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 12 5.21 5 S 28 5.16 5 C 9845 2.51 5 N 3449 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18521 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 35, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 170} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.09, per 1000 atoms: 0.60 Number of scatterers: 18521 At special positions: 0 Unit cell: (118.265, 116.095, 159.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 12 11.99 O 4730 8.00 N 3449 7.00 C 9845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.60 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 48.5% alpha, 14.3% beta 116 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 9.46 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 103 through 124 Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.225A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.619A pdb=" N ALA C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.573A pdb=" N ALA G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.284A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.663A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.516A pdb=" N SER G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 148 removed outlier: 3.613A pdb=" N ALA G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA G 147 " --> pdb=" O ARG G 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 3.996A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 32 removed outlier: 3.509A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 removed outlier: 4.240A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.582A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 63 removed outlier: 3.624A pdb=" N ILE M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 4.405A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 19 Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 49 Processing helix chain 'N' and resid 50 through 51 No H-bonds generated for 'chain 'N' and resid 50 through 51' Processing helix chain 'N' and resid 52 through 56 Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.898A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.721A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 58 Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 171 removed outlier: 5.738A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 11 removed outlier: 6.419A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 45 through 52 Processing sheet with id=AA8, first strand: chain 'J' and resid 45 through 52 removed outlier: 3.817A pdb=" N LYS N 97 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.318A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 8.74 Time building geometry restraints manager: 13.24 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: 2828 1.33 - 1.45: 7327 1.45 - 1.57: 8682 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19801 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.468 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.457 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" N GLY M 26 " pdb=" CA GLY M 26 " ideal model delta sigma weight residual 1.443 1.474 -0.031 8.60e-03 1.35e+04 1.28e+01 bond pdb=" C6 2MG 11207 " pdb=" N1 2MG 11207 " ideal model delta sigma weight residual 1.399 1.328 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C SER N 55 " pdb=" N SER N 56 " ideal model delta sigma weight residual 1.330 1.280 0.050 1.47e-02 4.63e+03 1.17e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.93: 2994 106.93 - 114.27: 12253 114.27 - 121.61: 9175 121.61 - 128.95: 3982 128.95 - 136.29: 545 Bond angle restraints: 28949 Sorted by residual: angle pdb=" N SER I 93 " pdb=" CA SER I 93 " pdb=" C SER I 93 " ideal model delta sigma weight residual 113.88 105.93 7.95 1.23e+00 6.61e-01 4.18e+01 angle pdb=" O3' C 11103 " pdb=" C3' C 11103 " pdb=" C2' C 11103 " ideal model delta sigma weight residual 113.70 121.69 -7.99 1.50e+00 4.44e-01 2.83e+01 angle pdb=" O3' A 11157 " pdb=" C3' A 11157 " pdb=" C2' A 11157 " ideal model delta sigma weight residual 109.50 101.96 7.54 1.50e+00 4.44e-01 2.52e+01 angle pdb=" CA SER M 46 " pdb=" C SER M 46 " pdb=" O SER M 46 " ideal model delta sigma weight residual 121.56 116.31 5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" N GLY N 68 " pdb=" CA GLY N 68 " pdb=" C GLY N 68 " ideal model delta sigma weight residual 115.72 108.87 6.85 1.51e+00 4.39e-01 2.06e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 11184 35.78 - 71.56: 1290 71.56 - 107.34: 169 107.34 - 143.12: 4 143.12 - 178.90: 4 Dihedral angle restraints: 12651 sinusoidal: 9481 harmonic: 3170 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual 200.00 33.90 166.10 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual -128.00 50.90 -178.90 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 232.00 54.69 177.31 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3191 0.077 - 0.154: 328 0.154 - 0.231: 79 0.231 - 0.308: 9 0.308 - 0.385: 2 Chirality restraints: 3609 Sorted by residual: chirality pdb=" C3' C 11103 " pdb=" C4' C 11103 " pdb=" O3' C 11103 " pdb=" C2' C 11103 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE J 49 " pdb=" N PHE J 49 " pdb=" C PHE J 49 " pdb=" CB PHE J 49 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' A 1 969 " pdb=" C4' A 1 969 " pdb=" O3' A 1 969 " pdb=" C2' A 1 969 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3606 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " -0.048 2.00e-02 2.50e+03 9.87e-02 3.17e+02 pdb=" N9 2MG 11207 " -0.020 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " 0.052 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " 0.072 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " 0.021 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " 0.004 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " 0.051 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " -0.047 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " -0.097 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " -0.142 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " -0.084 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " -0.032 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " 0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 26 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C PHE G 26 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE G 26 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL G 27 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 120 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C LEU G 120 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU G 120 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA G 121 " 0.016 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 55 2.20 - 2.87: 7424 2.87 - 3.55: 35090 3.55 - 4.22: 60082 4.22 - 4.90: 80301 Nonbonded interactions: 182952 Sorted by model distance: nonbonded pdb=" O3' U 1 952 " pdb="MG MG 11608 " model vdw 1.519 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11610 " model vdw 1.629 2.170 nonbonded pdb=" OP1 A 1 964 " pdb="MG MG 11611 " model vdw 1.659 2.170 nonbonded pdb=" OP2 C 1 972 " pdb="MG MG 11607 " model vdw 1.697 2.170 nonbonded pdb=" OP1 C 11109 " pdb="MG MG 11604 " model vdw 1.732 2.170 ... (remaining 182947 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 group one per residue 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 68.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 0.086 19801 Z= 0.435 Angle : 0.892 10.265 28949 Z= 0.551 Chirality : 0.053 0.385 3609 Planarity : 0.005 0.099 1995 Dihedral : 23.874 178.902 10599 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 42.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1092 helix: -1.23 (0.22), residues: 480 sheet: -2.30 (0.36), residues: 161 loop : -2.40 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 34 HIS 0.007 0.002 HIS M 12 PHE 0.019 0.002 PHE C 37 TYR 0.011 0.002 TYR N 20 ARG 0.008 0.001 ARG I 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.9250 (mt) cc_final: 0.9009 (tp) REVERT: B 139 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7395 (mtt180) REVERT: C 102 ASN cc_start: 0.9455 (t0) cc_final: 0.9198 (m110) REVERT: C 129 MET cc_start: 0.8870 (mmm) cc_final: 0.8228 (tpp) REVERT: C 181 ASP cc_start: 0.9054 (t0) cc_final: 0.8352 (p0) REVERT: C 203 PHE cc_start: 0.9076 (t80) cc_final: 0.8699 (t80) REVERT: G 91 VAL cc_start: 0.7421 (p) cc_final: 0.7214 (p) REVERT: I 32 GLN cc_start: 0.8757 (mm110) cc_final: 0.8550 (mm-40) REVERT: I 57 MET cc_start: 0.9379 (ptm) cc_final: 0.9090 (mmm) REVERT: I 110 GLN cc_start: 0.9585 (pt0) cc_final: 0.8756 (pm20) REVERT: I 112 GLU cc_start: 0.8217 (tt0) cc_final: 0.7747 (mp0) REVERT: J 19 ASP cc_start: 0.9199 (m-30) cc_final: 0.8948 (m-30) REVERT: J 53 ILE cc_start: 0.9181 (pt) cc_final: 0.8954 (tt) REVERT: J 63 ASP cc_start: 0.8579 (t0) cc_final: 0.7683 (t0) REVERT: J 65 TYR cc_start: 0.8477 (m-80) cc_final: 0.8087 (m-80) REVERT: M 27 LYS cc_start: 0.9409 (tppt) cc_final: 0.8784 (tppt) REVERT: M 31 LYS cc_start: 0.9248 (pttm) cc_final: 0.8923 (pttp) REVERT: M 50 GLU cc_start: 0.9519 (pm20) cc_final: 0.9140 (tm-30) REVERT: M 68 ASP cc_start: 0.9530 (m-30) cc_final: 0.9002 (t0) REVERT: M 95 LEU cc_start: 0.8930 (mt) cc_final: 0.8357 (mt) REVERT: N 86 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8742 (mt-10) REVERT: N 101 TRP cc_start: 0.8402 (p90) cc_final: 0.6002 (p90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3595 time to fit residues: 124.3890 Evaluate side-chains 156 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 78 optimal weight: 0.0270 chunk 61 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 138 optimal weight: 0.0270 overall best weight: 3.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 227 GLN G 122 ASN J 70 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19801 Z= 0.250 Angle : 0.694 7.548 28949 Z= 0.354 Chirality : 0.039 0.238 3609 Planarity : 0.006 0.060 1995 Dihedral : 24.781 176.968 8374 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1092 helix: -0.46 (0.22), residues: 501 sheet: -1.77 (0.37), residues: 155 loop : -1.81 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 96 HIS 0.007 0.001 HIS M 14 PHE 0.016 0.002 PHE S 74 TYR 0.011 0.002 TYR I 6 ARG 0.007 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.9580 (t0) cc_final: 0.9181 (m110) REVERT: C 129 MET cc_start: 0.8807 (mmm) cc_final: 0.8115 (tpp) REVERT: C 142 MET cc_start: 0.9187 (tpp) cc_final: 0.8963 (tpt) REVERT: C 168 TYR cc_start: 0.7972 (t80) cc_final: 0.7760 (t80) REVERT: C 181 ASP cc_start: 0.8922 (t0) cc_final: 0.8224 (p0) REVERT: C 203 PHE cc_start: 0.9006 (t80) cc_final: 0.8583 (t80) REVERT: C 211 MET cc_start: 0.7780 (tpp) cc_final: 0.7546 (tpp) REVERT: I 42 GLU cc_start: 0.9053 (tp30) cc_final: 0.8669 (tp30) REVERT: I 46 MET cc_start: 0.9299 (mmp) cc_final: 0.8786 (mmp) REVERT: I 110 GLN cc_start: 0.9523 (pt0) cc_final: 0.8733 (pm20) REVERT: I 112 GLU cc_start: 0.8193 (tt0) cc_final: 0.7560 (mp0) REVERT: I 115 LYS cc_start: 0.9071 (mttt) cc_final: 0.8674 (mttt) REVERT: I 118 LEU cc_start: 0.9545 (mm) cc_final: 0.9331 (mt) REVERT: J 19 ASP cc_start: 0.9264 (m-30) cc_final: 0.9014 (m-30) REVERT: J 63 ASP cc_start: 0.8064 (t0) cc_final: 0.7582 (t0) REVERT: J 90 LEU cc_start: 0.8611 (tp) cc_final: 0.8311 (tp) REVERT: M 12 HIS cc_start: 0.8761 (p90) cc_final: 0.8397 (p-80) REVERT: M 50 GLU cc_start: 0.9480 (pm20) cc_final: 0.9127 (tm-30) REVERT: M 81 MET cc_start: 0.9066 (mtt) cc_final: 0.8861 (mtt) REVERT: N 47 LYS cc_start: 0.9591 (tmtt) cc_final: 0.9185 (ptpp) REVERT: S 66 MET cc_start: 0.9275 (mtp) cc_final: 0.9071 (mtp) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.3625 time to fit residues: 108.3214 Evaluate side-chains 143 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS C 140 ASN G 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19801 Z= 0.213 Angle : 0.634 11.818 28949 Z= 0.320 Chirality : 0.037 0.251 3609 Planarity : 0.005 0.065 1995 Dihedral : 24.596 179.007 8374 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1092 helix: -0.14 (0.22), residues: 509 sheet: -1.42 (0.38), residues: 155 loop : -1.54 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.005 0.001 HIS B 168 PHE 0.015 0.002 PHE B 90 TYR 0.011 0.002 TYR G 44 ARG 0.007 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.7410 (tpt) cc_final: 0.6773 (tpp) REVERT: B 50 PHE cc_start: 0.6779 (t80) cc_final: 0.6450 (t80) REVERT: B 94 HIS cc_start: 0.7154 (t70) cc_final: 0.6939 (t70) REVERT: C 102 ASN cc_start: 0.9590 (t0) cc_final: 0.9255 (m110) REVERT: C 129 MET cc_start: 0.8749 (mmm) cc_final: 0.8085 (tpp) REVERT: C 168 TYR cc_start: 0.7859 (t80) cc_final: 0.7646 (t80) REVERT: C 181 ASP cc_start: 0.8906 (t0) cc_final: 0.8269 (p0) REVERT: G 38 THR cc_start: 0.8884 (p) cc_final: 0.8642 (t) REVERT: I 110 GLN cc_start: 0.9514 (pt0) cc_final: 0.8963 (pm20) REVERT: J 18 ILE cc_start: 0.9608 (tp) cc_final: 0.9401 (tt) REVERT: J 19 ASP cc_start: 0.9300 (m-30) cc_final: 0.9033 (m-30) REVERT: J 63 ASP cc_start: 0.8541 (t0) cc_final: 0.7668 (t0) REVERT: J 65 TYR cc_start: 0.8673 (m-80) cc_final: 0.8393 (m-80) REVERT: M 12 HIS cc_start: 0.8772 (p90) cc_final: 0.8439 (p-80) REVERT: M 27 LYS cc_start: 0.9297 (tppt) cc_final: 0.8861 (tppt) REVERT: M 50 GLU cc_start: 0.9477 (pm20) cc_final: 0.9149 (tm-30) REVERT: N 74 LEU cc_start: 0.9421 (tt) cc_final: 0.9192 (tt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3436 time to fit residues: 94.8052 Evaluate side-chains 139 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN N 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19801 Z= 0.246 Angle : 0.642 8.491 28949 Z= 0.325 Chirality : 0.037 0.230 3609 Planarity : 0.005 0.070 1995 Dihedral : 24.558 179.430 8374 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.24), residues: 1092 helix: -0.09 (0.22), residues: 509 sheet: -1.18 (0.37), residues: 161 loop : -1.51 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 103 HIS 0.015 0.002 HIS S 14 PHE 0.013 0.002 PHE B 184 TYR 0.010 0.002 TYR B 213 ARG 0.006 0.001 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LYS cc_start: 0.6014 (tptt) cc_final: 0.5621 (tppt) REVERT: B 50 PHE cc_start: 0.6866 (t80) cc_final: 0.6591 (t80) REVERT: B 94 HIS cc_start: 0.7023 (t70) cc_final: 0.6627 (t70) REVERT: B 113 ARG cc_start: 0.8584 (mtm180) cc_final: 0.8016 (mtm180) REVERT: C 102 ASN cc_start: 0.9584 (t0) cc_final: 0.9280 (m110) REVERT: C 129 MET cc_start: 0.8765 (mmm) cc_final: 0.8133 (tpp) REVERT: C 134 MET cc_start: 0.8679 (ptm) cc_final: 0.8461 (ptm) REVERT: C 150 LYS cc_start: 0.8710 (tttm) cc_final: 0.8353 (tptp) REVERT: C 168 TYR cc_start: 0.7995 (t80) cc_final: 0.7271 (t80) REVERT: C 181 ASP cc_start: 0.8873 (t0) cc_final: 0.8247 (p0) REVERT: C 211 MET cc_start: 0.7666 (tpp) cc_final: 0.7341 (tpp) REVERT: G 15 ASP cc_start: 0.7529 (t70) cc_final: 0.7287 (t0) REVERT: G 40 GLU cc_start: 0.8259 (pp20) cc_final: 0.7988 (mt-10) REVERT: G 104 ILE cc_start: 0.8106 (tp) cc_final: 0.7895 (tp) REVERT: I 110 GLN cc_start: 0.9530 (pt0) cc_final: 0.8982 (pm20) REVERT: I 112 GLU cc_start: 0.8287 (tt0) cc_final: 0.7618 (tm-30) REVERT: I 118 LEU cc_start: 0.9194 (mt) cc_final: 0.8987 (mt) REVERT: J 63 ASP cc_start: 0.8481 (t0) cc_final: 0.8086 (t70) REVERT: M 12 HIS cc_start: 0.8755 (p90) cc_final: 0.8390 (p-80) REVERT: M 27 LYS cc_start: 0.9308 (tppt) cc_final: 0.8863 (tppt) REVERT: M 50 GLU cc_start: 0.9507 (pm20) cc_final: 0.9193 (tm-30) REVERT: M 81 MET cc_start: 0.9067 (mtt) cc_final: 0.8586 (mmm) REVERT: N 6 MET cc_start: 0.9152 (mmm) cc_final: 0.8874 (mmm) REVERT: N 74 LEU cc_start: 0.9446 (tt) cc_final: 0.9143 (tt) REVERT: N 77 PHE cc_start: 0.9555 (m-10) cc_final: 0.9343 (m-10) REVERT: S 17 LYS cc_start: 0.9528 (mptt) cc_final: 0.9325 (mttt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3239 time to fit residues: 84.7723 Evaluate side-chains 142 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19801 Z= 0.248 Angle : 0.642 9.054 28949 Z= 0.326 Chirality : 0.037 0.234 3609 Planarity : 0.006 0.074 1995 Dihedral : 24.567 179.029 8374 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1092 helix: -0.10 (0.22), residues: 508 sheet: -1.07 (0.38), residues: 163 loop : -1.41 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 101 HIS 0.007 0.001 HIS S 14 PHE 0.015 0.002 PHE B 126 TYR 0.009 0.001 TYR J 65 ARG 0.013 0.001 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LYS cc_start: 0.6006 (tptt) cc_final: 0.5690 (tppt) REVERT: B 94 HIS cc_start: 0.6972 (t70) cc_final: 0.6522 (t70) REVERT: B 109 GLN cc_start: 0.8652 (tt0) cc_final: 0.8451 (tt0) REVERT: B 113 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8067 (mtm180) REVERT: C 102 ASN cc_start: 0.9576 (t0) cc_final: 0.9301 (m110) REVERT: C 129 MET cc_start: 0.8712 (mmm) cc_final: 0.8089 (tpp) REVERT: C 181 ASP cc_start: 0.8874 (t0) cc_final: 0.8240 (p0) REVERT: G 15 ASP cc_start: 0.7326 (t70) cc_final: 0.7050 (t70) REVERT: I 52 LEU cc_start: 0.9473 (tt) cc_final: 0.9249 (pp) REVERT: I 88 MET cc_start: 0.9391 (mmp) cc_final: 0.9058 (mmp) REVERT: I 110 GLN cc_start: 0.9512 (pt0) cc_final: 0.8943 (pm20) REVERT: I 112 GLU cc_start: 0.8290 (tt0) cc_final: 0.7651 (tm-30) REVERT: I 118 LEU cc_start: 0.9209 (mt) cc_final: 0.8997 (mt) REVERT: I 130 ARG cc_start: 0.7804 (mtt-85) cc_final: 0.7551 (mtm-85) REVERT: J 19 ASP cc_start: 0.9208 (m-30) cc_final: 0.8921 (m-30) REVERT: J 63 ASP cc_start: 0.8549 (t0) cc_final: 0.8106 (t0) REVERT: M 12 HIS cc_start: 0.8728 (p90) cc_final: 0.8368 (p-80) REVERT: M 27 LYS cc_start: 0.9303 (tppt) cc_final: 0.8863 (tppt) REVERT: M 50 GLU cc_start: 0.9523 (pm20) cc_final: 0.9211 (tm-30) REVERT: M 81 MET cc_start: 0.9155 (mtt) cc_final: 0.8765 (mtt) REVERT: N 6 MET cc_start: 0.9127 (mmm) cc_final: 0.8895 (mmm) REVERT: N 74 LEU cc_start: 0.9439 (tt) cc_final: 0.9170 (tt) REVERT: S 17 LYS cc_start: 0.9550 (mptt) cc_final: 0.9343 (mttt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.3393 time to fit residues: 87.0428 Evaluate side-chains 130 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 142 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4217 Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: Processing file: --standard input-- Building His ring NH Hydrogens. Building or keeping OH & SH Hydrogens. Rotating existing OH & SH Hydrogens WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HN41 from 5MC will be treated as hydrogen WARNING: atom HN41 from 5MC will be treated as hydrogen WARNING: atom HN42 from 5MC will be treated as hydrogen WARNING: atom HN42 from 5MC will be treated as hydrogen WARNING: atom HN41 from 5MC will be treated as hydrogen WARNING: atom HN42 from 5MC will be treated as hydrogen WARNING: atom HN42 from 5MC will be treated as hydrogen WARNING: atom HN41 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen VDW dot density = 16/A^2 Orientation penalty scale = 9999 (999900%) Eliminate contacts within 3 bonds. Ignore atoms with |occupancy| <= 0.01 during adjustments. Waters ignored if B-Factor >= 40 or |occupancy| < 0.66 Aromatic rings in amino acids accept hydrogen bonds. Flipping Asn, Gln and His groups. For each flip state, bumps where gap is more than 0.4A are indicated with '!'. Rotating NH3 Hydrogens. Not processing Met methyls.