Starting phenix.real_space_refine on Sat Mar 16 09:13:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/03_2024/6pcs_20306_neut_updated.pdb" } resolution = 2.8 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= -0.010 sd= 1.420 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 3015 5.49 5 S 22 5.16 5 C 33528 2.51 5 N 13324 2.21 5 O 22277 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 35": "OE1" <-> "OE2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ASP 187": "OD1" <-> "OD2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ASP 264": "OD1" <-> "OD2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72169 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'O8S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 29.39, per 1000 atoms: 0.41 Number of scatterers: 72169 At special positions: 0 Unit cell: (227.783, 221.984, 189.681, 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 22 16.00 P 3015 15.00 F 3 9.00 O 22277 8.00 N 13324 7.00 C 33528 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 34.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 12 sheets defined 17.9% alpha, 13.1% beta 889 base pairs and 1655 stacking pairs defined. Time for finding SS restraints: 40.56 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 209 through 213 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 85 removed outlier: 4.447A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 95 No H-bonds generated for 'chain 'L' and resid 92 through 95' Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 removed outlier: 3.563A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.879A pdb=" N LEU M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.574A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 71 removed outlier: 3.847A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.430A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 66 through 71 removed outlier: 4.384A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 107 Proline residue: O 97 - end of helix removed outlier: 4.514A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 4.258A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.653A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.602A pdb=" N LEU K 130 " --> pdb=" O ALA K 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.902A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.497A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= H, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.320A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 169 through 172 removed outlier: 3.528A pdb=" N LYS N 204 " --> pdb=" O ASP N 108 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.457A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.460A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 73 through 76 removed outlier: 3.637A pdb=" N ALA O 87 " --> pdb=" O TYR O 74 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2203 hydrogen bonds 3594 hydrogen bond angles 0 basepair planarities 889 basepair parallelities 1655 stacking parallelities Total time for adding SS restraints: 129.33 Time building geometry restraints manager: 36.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7200 1.33 - 1.45: 38321 1.45 - 1.57: 28434 1.57 - 1.69: 6047 1.69 - 1.81: 42 Bond restraints: 80044 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.364 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.347 -0.192 2.00e-02 2.50e+03 9.26e+01 ... (remaining 80039 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.72: 17915 106.72 - 113.74: 49220 113.74 - 120.77: 32870 120.77 - 127.80: 18143 127.80 - 134.82: 5087 Bond angle restraints: 123235 Sorted by residual: angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 125.98 -19.66 3.00e+00 1.11e-01 4.29e+01 angle pdb=" N GLN N 150 " pdb=" CA GLN N 150 " pdb=" C GLN N 150 " ideal model delta sigma weight residual 111.71 119.16 -7.45 1.15e+00 7.56e-01 4.19e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C4 OMG I2251 " ideal model delta sigma weight residual 108.29 126.88 -18.59 3.00e+00 1.11e-01 3.84e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C8 OMG I2251 " ideal model delta sigma weight residual 142.82 125.70 17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" C1' 2MG I2445 " pdb=" N9 2MG I2445 " pdb=" C8 2MG I2445 " ideal model delta sigma weight residual 110.07 125.94 -15.87 3.00e+00 1.11e-01 2.80e+01 ... (remaining 123230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 44153 35.80 - 71.60: 6626 71.60 - 107.40: 786 107.40 - 143.20: 5 143.20 - 179.00: 7 Dihedral angle restraints: 51577 sinusoidal: 48887 harmonic: 2690 Sorted by residual: dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 49.98 -177.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 42.59 -170.59 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' U I1313 " pdb=" C1' U I1313 " pdb=" N1 U I1313 " pdb=" C2 U I1313 " ideal model delta sinusoidal sigma weight residual 200.00 88.58 111.42 1 1.50e+01 4.44e-03 5.82e+01 ... (remaining 51574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 15879 0.055 - 0.111: 256 0.111 - 0.166: 19 0.166 - 0.222: 2 0.222 - 0.277: 1 Chirality restraints: 16157 Sorted by residual: chirality pdb=" CA GLN N 150 " pdb=" N GLN N 150 " pdb=" C GLN N 150 " pdb=" CB GLN N 150 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA SER M 80 " pdb=" N SER M 80 " pdb=" C SER M 80 " pdb=" CB SER M 80 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA VAL M 83 " pdb=" N VAL M 83 " pdb=" C VAL M 83 " pdb=" CB VAL M 83 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 16154 not shown) Planarity restraints: 4345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.031 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' 2MG I2445 " -0.457 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.738 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.582 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.222 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.898 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.203 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.933 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.047 2.00e-02 2.50e+03 5.94e-01 7.95e+03 pdb=" C4' OMG I2251 " 0.444 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.672 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.608 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.199 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.938 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.217 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.913 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.045 2.00e-02 2.50e+03 5.76e-01 7.46e+03 pdb=" C4' 2MG I1835 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.625 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.583 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.201 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.920 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.229 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.875 2.00e-02 2.50e+03 ... (remaining 4342 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 126 2.31 - 2.96: 28597 2.96 - 3.60: 121426 3.60 - 4.25: 227066 4.25 - 4.90: 294050 Nonbonded interactions: 671265 Sorted by model distance: nonbonded pdb=" N3 G I2032 " pdb=" NE2 GLN N 150 " model vdw 1.658 2.600 nonbonded pdb=" O2' A I1084 " pdb=" O2' U I1105 " model vdw 1.911 2.440 nonbonded pdb=" C4 G I2032 " pdb=" NE2 GLN N 150 " model vdw 1.930 3.340 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.989 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 2.009 2.440 ... (remaining 671260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 11.410 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: 0.070 Extract box with map and model: 44.530 Check model and map are aligned: 0.840 Set scattering table: 0.500 Process input model: 278.380 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.150 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 348.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.005 0.391 80044 Z= 0.317 Angle : 0.376 19.661 123235 Z= 0.196 Chirality : 0.024 0.277 16157 Planarity : 0.022 0.597 4345 Dihedral : 23.639 179.000 49865 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 1.31 % Allowed : 13.87 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.23), residues: 957 helix: -3.40 (0.28), residues: 161 sheet: -2.58 (0.33), residues: 172 loop : -2.44 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 78 HIS 0.003 0.001 HIS K 230 PHE 0.005 0.001 PHE N 156 TYR 0.006 0.001 TYR L 58 ARG 0.002 0.000 ARG M 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 229 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 255 LYS cc_start: 0.8492 (tttm) cc_final: 0.8263 (ttmm) REVERT: L 4 ASN cc_start: 0.8828 (p0) cc_final: 0.8505 (p0) REVERT: L 91 ASP cc_start: 0.8322 (t0) cc_final: 0.8091 (t0) REVERT: L 117 THR cc_start: 0.8263 (p) cc_final: 0.7971 (t) REVERT: M 155 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: N 108 ASP cc_start: 0.7619 (m-30) cc_final: 0.7224 (p0) REVERT: N 150 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: O 58 ASN cc_start: 0.8403 (m-40) cc_final: 0.8167 (m-40) outliers start: 10 outliers final: 1 residues processed: 237 average time/residue: 1.8220 time to fit residues: 551.2756 Evaluate side-chains 147 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 150 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 0.4980 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 2.9990 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 134 ASN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN N 49 GLN N 58 ASN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 GLN O 135 GLN O 138 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 80044 Z= 0.442 Angle : 0.740 16.303 123235 Z= 0.379 Chirality : 0.039 0.325 16157 Planarity : 0.007 0.140 4345 Dihedral : 23.492 174.966 48066 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.96 % Favored : 93.83 % Rotamer: Outliers : 5.76 % Allowed : 21.60 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.73 (0.25), residues: 957 helix: -2.05 (0.33), residues: 180 sheet: -1.63 (0.36), residues: 195 loop : -1.83 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.009 0.002 HIS K 200 PHE 0.010 0.002 PHE M 158 TYR 0.016 0.002 TYR K 103 ARG 0.008 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7807 (mp0) cc_final: 0.7231 (tp30) REVERT: K 66 ASP cc_start: 0.7970 (t0) cc_final: 0.7764 (t0) REVERT: K 246 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8304 (p) REVERT: L 1 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7300 (ttp) REVERT: L 18 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7426 (mtm-85) REVERT: N 108 ASP cc_start: 0.7595 (m-30) cc_final: 0.7248 (p0) REVERT: N 165 MET cc_start: 0.8685 (ttt) cc_final: 0.8384 (ttt) REVERT: O 31 GLU cc_start: 0.7395 (tp30) cc_final: 0.6928 (mm-30) outliers start: 44 outliers final: 21 residues processed: 181 average time/residue: 1.6282 time to fit residues: 389.0210 Evaluate side-chains 160 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 45 ASN Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 246 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 359 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 chunk 320 optimal weight: 0.9980 chunk 356 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 80044 Z= 0.282 Angle : 0.606 14.863 123235 Z= 0.324 Chirality : 0.033 0.273 16157 Planarity : 0.007 0.130 4345 Dihedral : 23.531 176.083 48060 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.54 % Favored : 94.25 % Rotamer: Outliers : 5.63 % Allowed : 23.17 % Favored : 71.20 % 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: -1.86 (0.26), residues: 957 helix: -1.15 (0.37), residues: 177 sheet: -1.04 (0.37), residues: 195 loop : -1.33 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.008 0.001 PHE N 68 TYR 0.009 0.001 TYR K 103 ARG 0.007 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 157 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7773 (mp0) cc_final: 0.7252 (tp30) REVERT: K 66 ASP cc_start: 0.8043 (t0) cc_final: 0.7804 (t0) REVERT: K 271 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6056 (ptt-90) REVERT: L 1 MET cc_start: 0.7579 (ttp) cc_final: 0.7305 (ttp) REVERT: N 108 ASP cc_start: 0.7675 (m-30) cc_final: 0.7307 (p0) REVERT: O 1 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6490 (ttt) REVERT: O 31 GLU cc_start: 0.7545 (tp30) cc_final: 0.7021 (mm-30) outliers start: 43 outliers final: 20 residues processed: 187 average time/residue: 1.5564 time to fit residues: 386.7878 Evaluate side-chains 180 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 0.9980 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 360 optimal weight: 7.9990 chunk 381 optimal weight: 0.0370 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 86 ASN K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 80044 Z= 0.391 Angle : 0.682 14.791 123235 Z= 0.356 Chirality : 0.037 0.303 16157 Planarity : 0.007 0.137 4345 Dihedral : 23.584 177.163 48060 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.69 % Favored : 93.00 % Rotamer: Outliers : 5.10 % Allowed : 25.00 % Favored : 69.90 % 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: -1.68 (0.26), residues: 957 helix: -1.11 (0.37), residues: 179 sheet: -0.94 (0.37), residues: 195 loop : -1.16 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 78 HIS 0.004 0.001 HIS O 76 PHE 0.011 0.001 PHE M 23 TYR 0.007 0.001 TYR O 125 ARG 0.006 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7832 (mp0) cc_final: 0.7303 (tp30) REVERT: K 66 ASP cc_start: 0.8139 (t0) cc_final: 0.7907 (t0) REVERT: K 133 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.8006 (ttm-80) REVERT: K 271 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6093 (ptt-90) REVERT: L 1 MET cc_start: 0.7554 (ttp) cc_final: 0.7309 (ttp) REVERT: M 155 GLU cc_start: 0.7387 (pp20) cc_final: 0.6987 (tt0) REVERT: N 108 ASP cc_start: 0.7585 (m-30) cc_final: 0.7288 (p0) REVERT: O 1 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6519 (ttt) REVERT: O 31 GLU cc_start: 0.7594 (tp30) cc_final: 0.7111 (mm-30) outliers start: 39 outliers final: 28 residues processed: 185 average time/residue: 1.6873 time to fit residues: 408.8957 Evaluate side-chains 181 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 133 ARG Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 2.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 342 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 80044 Z= 0.496 Angle : 0.779 15.352 123235 Z= 0.401 Chirality : 0.043 0.337 16157 Planarity : 0.008 0.141 4345 Dihedral : 23.826 178.026 48060 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.00 % Favored : 92.69 % Rotamer: Outliers : 6.41 % Allowed : 23.95 % Favored : 69.63 % 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: -1.80 (0.26), residues: 957 helix: -1.27 (0.36), residues: 179 sheet: -0.88 (0.40), residues: 170 loop : -1.27 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.005 0.001 HIS O 77 PHE 0.016 0.002 PHE M 23 TYR 0.009 0.002 TYR K 161 ARG 0.006 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7921 (mp0) cc_final: 0.7304 (tp30) REVERT: K 66 ASP cc_start: 0.8189 (t0) cc_final: 0.7880 (t0) REVERT: K 246 THR cc_start: 0.8773 (t) cc_final: 0.8569 (p) REVERT: K 271 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6187 (ptt-90) REVERT: L 1 MET cc_start: 0.7541 (ttp) cc_final: 0.7258 (ttp) REVERT: M 155 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: N 108 ASP cc_start: 0.7571 (m-30) cc_final: 0.7279 (p0) REVERT: N 181 ASP cc_start: 0.8167 (t0) cc_final: 0.7962 (t0) REVERT: O 1 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6636 (ttt) REVERT: O 31 GLU cc_start: 0.7581 (tp30) cc_final: 0.7125 (mm-30) REVERT: O 92 MET cc_start: 0.8613 (mtp) cc_final: 0.8406 (tpp) outliers start: 49 outliers final: 29 residues processed: 183 average time/residue: 1.6184 time to fit residues: 391.5672 Evaluate side-chains 176 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 6.9990 chunk 343 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 317 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 80044 Z= 0.236 Angle : 0.631 14.963 123235 Z= 0.339 Chirality : 0.035 0.303 16157 Planarity : 0.007 0.129 4345 Dihedral : 23.823 177.931 48060 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 6.15 % Allowed : 25.79 % Favored : 68.06 % 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: -1.51 (0.26), residues: 957 helix: -0.96 (0.37), residues: 184 sheet: -0.73 (0.40), residues: 161 loop : -1.10 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 78 HIS 0.011 0.002 HIS K 200 PHE 0.016 0.001 PHE M 23 TYR 0.011 0.001 TYR O 53 ARG 0.009 0.001 ARG K 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7920 (mp0) cc_final: 0.7430 (tp30) REVERT: K 66 ASP cc_start: 0.8073 (t0) cc_final: 0.7783 (t0) REVERT: K 177 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7334 (mmm-85) REVERT: K 271 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6113 (ptt-90) REVERT: L 1 MET cc_start: 0.7462 (ttp) cc_final: 0.7237 (ttp) REVERT: L 17 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8142 (mttt) REVERT: M 1 MET cc_start: 0.7400 (ttt) cc_final: 0.7098 (ttt) REVERT: M 115 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: M 155 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: N 108 ASP cc_start: 0.7454 (m-30) cc_final: 0.7230 (p0) REVERT: O 31 GLU cc_start: 0.7587 (tp30) cc_final: 0.7124 (mm-30) REVERT: O 92 MET cc_start: 0.8570 (mtp) cc_final: 0.8341 (tpp) outliers start: 47 outliers final: 31 residues processed: 191 average time/residue: 1.6406 time to fit residues: 412.8954 Evaluate side-chains 191 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 115 GLN Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 chunk 321 optimal weight: 0.9980 chunk 213 optimal weight: 30.0000 chunk 380 optimal weight: 0.0970 chunk 238 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 80044 Z= 0.416 Angle : 0.710 15.198 123235 Z= 0.370 Chirality : 0.039 0.309 16157 Planarity : 0.007 0.138 4345 Dihedral : 23.754 178.121 48060 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.11 % Favored : 92.58 % Rotamer: Outliers : 6.68 % Allowed : 26.05 % Favored : 67.28 % 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: -1.57 (0.26), residues: 957 helix: -1.00 (0.37), residues: 185 sheet: -0.81 (0.40), residues: 162 loop : -1.13 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 78 HIS 0.004 0.001 HIS O 80 PHE 0.017 0.001 PHE M 23 TYR 0.009 0.001 TYR O 125 ARG 0.008 0.001 ARG K 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7880 (mp0) cc_final: 0.7317 (tp30) REVERT: K 66 ASP cc_start: 0.8137 (t0) cc_final: 0.7860 (t0) REVERT: K 177 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7415 (mmm-85) REVERT: K 271 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6239 (ptt-90) REVERT: L 1 MET cc_start: 0.7476 (ttp) cc_final: 0.7273 (ttp) REVERT: L 17 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8215 (mttt) REVERT: M 155 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: N 108 ASP cc_start: 0.7477 (m-30) cc_final: 0.7262 (p0) REVERT: O 31 GLU cc_start: 0.7627 (tp30) cc_final: 0.7160 (mm-30) REVERT: O 92 MET cc_start: 0.8620 (mtp) cc_final: 0.8394 (tpp) outliers start: 51 outliers final: 34 residues processed: 179 average time/residue: 1.5396 time to fit residues: 367.5720 Evaluate side-chains 179 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 80044 Z= 0.546 Angle : 0.812 15.584 123235 Z= 0.413 Chirality : 0.044 0.340 16157 Planarity : 0.008 0.145 4345 Dihedral : 23.848 178.537 48060 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.42 % Favored : 92.27 % Rotamer: Outliers : 6.41 % Allowed : 26.83 % Favored : 66.75 % 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: -1.76 (0.26), residues: 957 helix: -1.21 (0.36), residues: 185 sheet: -0.92 (0.40), residues: 162 loop : -1.23 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.006 0.002 HIS M 165 PHE 0.021 0.002 PHE M 23 TYR 0.012 0.002 TYR O 125 ARG 0.007 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 147 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7979 (mp0) cc_final: 0.7431 (tp30) REVERT: K 66 ASP cc_start: 0.8196 (t0) cc_final: 0.7902 (t0) REVERT: K 177 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7393 (mmm-85) REVERT: K 271 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6359 (ptt-90) REVERT: L 115 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: M 155 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: N 49 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: N 108 ASP cc_start: 0.7488 (m-30) cc_final: 0.7256 (p0) REVERT: N 181 ASP cc_start: 0.8175 (t0) cc_final: 0.7948 (t0) REVERT: O 31 GLU cc_start: 0.7679 (tp30) cc_final: 0.7207 (mm-30) outliers start: 49 outliers final: 35 residues processed: 181 average time/residue: 1.5780 time to fit residues: 379.6243 Evaluate side-chains 185 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 145 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 354 optimal weight: 0.6980 chunk 213 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 chunk 353 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 80044 Z= 0.241 Angle : 0.622 14.981 123235 Z= 0.333 Chirality : 0.033 0.292 16157 Planarity : 0.007 0.128 4345 Dihedral : 23.773 177.935 48060 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 4.58 % Allowed : 28.93 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.26), residues: 957 helix: -0.87 (0.38), residues: 185 sheet: -0.75 (0.40), residues: 163 loop : -1.06 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 80 HIS 0.004 0.001 HIS K 200 PHE 0.012 0.001 PHE M 23 TYR 0.018 0.001 TYR K 83 ARG 0.009 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7892 (mp0) cc_final: 0.7409 (tp30) REVERT: K 66 ASP cc_start: 0.8045 (t0) cc_final: 0.7789 (t0) REVERT: K 117 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7958 (tp40) REVERT: K 177 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7308 (mmm-85) REVERT: K 271 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6262 (ptt-90) REVERT: L 17 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8159 (mttt) REVERT: L 115 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7447 (pp20) REVERT: M 155 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: O 31 GLU cc_start: 0.7629 (tp30) cc_final: 0.7174 (mm-30) outliers start: 35 outliers final: 24 residues processed: 179 average time/residue: 1.5804 time to fit residues: 374.1425 Evaluate side-chains 189 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 99 ARG Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 10.0000 chunk 375 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 393 optimal weight: 0.8980 chunk 362 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 80044 Z= 0.321 Angle : 0.651 15.023 123235 Z= 0.345 Chirality : 0.035 0.292 16157 Planarity : 0.007 0.135 4345 Dihedral : 23.729 178.141 48060 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.21 % Favored : 92.58 % Rotamer: Outliers : 4.58 % Allowed : 29.32 % Favored : 66.10 % 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: -1.40 (0.27), residues: 957 helix: -0.78 (0.38), residues: 184 sheet: -0.67 (0.41), residues: 162 loop : -1.05 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.005 0.001 HIS K 200 PHE 0.017 0.001 PHE M 23 TYR 0.018 0.002 TYR K 83 ARG 0.014 0.001 ARG K 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7909 (mp0) cc_final: 0.7397 (tp30) REVERT: K 66 ASP cc_start: 0.8128 (t0) cc_final: 0.7861 (t0) REVERT: K 177 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7355 (mmm-85) REVERT: K 271 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6303 (ptt-90) REVERT: L 17 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8223 (mttt) REVERT: L 115 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7512 (pp20) REVERT: M 155 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: O 1 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6785 (ttt) REVERT: O 31 GLU cc_start: 0.7649 (tp30) cc_final: 0.7186 (mm-30) outliers start: 35 outliers final: 24 residues processed: 184 average time/residue: 1.6671 time to fit residues: 401.4495 Evaluate side-chains 181 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 128 ARG Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 322 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092455 restraints weight = 142761.402| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 0.65 r_work: 0.3102 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 80044 Z= 0.359 Angle : 0.679 15.230 123235 Z= 0.357 Chirality : 0.037 0.300 16157 Planarity : 0.007 0.136 4345 Dihedral : 23.746 177.862 48060 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.42 % Favored : 92.27 % Rotamer: Outliers : 4.71 % Allowed : 29.32 % Favored : 65.97 % 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: -1.47 (0.26), residues: 957 helix: -0.84 (0.38), residues: 184 sheet: -0.76 (0.40), residues: 162 loop : -1.08 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.005 0.001 HIS K 200 PHE 0.023 0.001 PHE M 23 TYR 0.020 0.002 TYR K 83 ARG 0.019 0.001 ARG K 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11604.78 seconds wall clock time: 208 minutes 14.10 seconds (12494.10 seconds total)