Starting phenix.real_space_refine on Fri Feb 16 23:24:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytf_10915/02_2024/6ytf_10915_updated.pdb" } resolution = 3.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 477 5.49 5 Mg 24 5.21 5 S 24 5.16 5 C 8747 2.51 5 N 3120 2.21 5 O 4514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 41": "OE1" <-> "OE2" Residue "d GLU 82": "OE1" <-> "OE2" Residue "d ASP 83": "OD1" <-> "OD2" Residue "d GLU 85": "OE1" <-> "OE2" Residue "d GLU 118": "OE1" <-> "OE2" Residue "d PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 152": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d ASP 181": "OD1" <-> "OD2" Residue "d ARG 188": "NH1" <-> "NH2" Residue "d PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 206": "OE1" <-> "OE2" Residue "h ARG 10": "NH1" <-> "NH2" Residue "h GLU 11": "OE1" <-> "OE2" Residue "h ASP 15": "OD1" <-> "OD2" Residue "h PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 48": "OE1" <-> "OE2" Residue "h ARG 49": "NH1" <-> "NH2" Residue "h GLU 52": "OE1" <-> "OE2" Residue "h ASP 57": "OD1" <-> "OD2" Residue "h GLU 60": "OE1" <-> "OE2" Residue "h PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 67": "OE1" <-> "OE2" Residue "h ARG 70": "NH1" <-> "NH2" Residue "h ARG 102": "NH1" <-> "NH2" Residue "h ARG 111": "NH1" <-> "NH2" Residue "h GLU 113": "OE1" <-> "OE2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "j TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 10": "NH1" <-> "NH2" Residue "j TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 40": "OE1" <-> "OE2" Residue "j TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 105": "OD1" <-> "OD2" Residue "j ARG 122": "NH1" <-> "NH2" Residue "k ASP 19": "OD1" <-> "OD2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k GLU 27": "OE1" <-> "OE2" Residue "k GLU 47": "OE1" <-> "OE2" Residue "k TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 81": "OD1" <-> "OD2" Residue "n ASP 11": "OD1" <-> "OD2" Residue "n TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 41": "OE1" <-> "OE2" Residue "n GLU 47": "OE1" <-> "OE2" Residue "n ASP 50": "OD1" <-> "OD2" Residue "n GLU 59": "OE1" <-> "OE2" Residue "n ASP 68": "OD1" <-> "OD2" Residue "n ASP 82": "OD1" <-> "OD2" Residue "n TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "o GLU 14": "OE1" <-> "OE2" Residue "o GLU 26": "OE1" <-> "OE2" Residue "o GLU 39": "OE1" <-> "OE2" Residue "o GLU 40": "OE1" <-> "OE2" Residue "o PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16906 Number of models: 1 Model: "" Number of chains: 12 Chain: "3" Number of atoms: 9676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 9676 Classifications: {'RNA': 453} Modifications used: {'rna2p_pur': 35, 'rna2p_pyr': 39, 'rna3p_pur': 208, 'rna3p_pyr': 171} Link IDs: {'rna2p': 74, 'rna3p': 378} Chain breaks: 1 Chain: "7" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 428 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "9" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Classifications: {'RNA': 4} Modifications used: {'rna3p_pyr': 4} Link IDs: {'rna3p': 3} Chain: "d" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1649 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "h" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "j" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "k" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 797 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "n" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "o" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 791 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 650 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "3" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 65 Unusual residues: {' MG': 23, 'T1C': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.51, per 1000 atoms: 0.56 Number of scatterers: 16906 At special positions: 0 Unit cell: (130.995, 138.45, 108.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 477 15.00 Mg 24 11.99 O 4514 8.00 N 3120 7.00 C 8747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 9.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 6 sheets defined 38.7% alpha, 12.4% beta 141 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 9.20 Creating SS restraints... Processing helix chain 'd' and resid 7 through 10 No H-bonds generated for 'chain 'd' and resid 7 through 10' Processing helix chain 'd' and resid 29 through 46 removed outlier: 3.731A pdb=" N VAL d 39 " --> pdb=" O LYS d 35 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS d 45 " --> pdb=" O GLU d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 77 Processing helix chain 'd' and resid 84 through 95 removed outlier: 4.159A pdb=" N ARG d 89 " --> pdb=" O GLU d 85 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE d 94 " --> pdb=" O GLU d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 113 through 126 removed outlier: 3.638A pdb=" N LYS d 126 " --> pdb=" O SER d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 143 Processing helix chain 'h' and resid 21 through 30 Processing helix chain 'h' and resid 36 through 52 removed outlier: 3.849A pdb=" N GLU h 52 " --> pdb=" O GLU h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 68 removed outlier: 3.660A pdb=" N GLU h 63 " --> pdb=" O VAL h 59 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU h 67 " --> pdb=" O GLU h 63 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS h 68 " --> pdb=" O THR h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 107 Processing helix chain 'h' and resid 116 through 128 removed outlier: 4.265A pdb=" N GLU h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 143 removed outlier: 3.816A pdb=" N ARG h 143 " --> pdb=" O ASP h 140 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 36 No H-bonds generated for 'chain 'j' and resid 33 through 36' Processing helix chain 'j' and resid 40 through 46 Processing helix chain 'j' and resid 49 through 52 No H-bonds generated for 'chain 'j' and resid 49 through 52' Processing helix chain 'j' and resid 70 through 88 Processing helix chain 'j' and resid 90 through 98 Proline residue: j 94 - end of helix Processing helix chain 'k' and resid 15 through 31 removed outlier: 3.749A pdb=" N GLN k 20 " --> pdb=" O ARG k 16 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU k 27 " --> pdb=" O GLN k 23 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR k 28 " --> pdb=" O GLU k 24 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 88 Processing helix chain 'n' and resid 15 through 21 removed outlier: 4.042A pdb=" N THR n 20 " --> pdb=" O VAL n 16 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR n 21 " --> pdb=" O ILE n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 45 through 47 No H-bonds generated for 'chain 'n' and resid 45 through 47' Processing helix chain 'n' and resid 50 through 62 removed outlier: 4.013A pdb=" N ASP n 54 " --> pdb=" O ASP n 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA n 55 " --> pdb=" O ALA n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 83 Processing helix chain 'n' and resid 86 through 92 Processing helix chain 'o' and resid 4 through 19 Processing helix chain 'o' and resid 21 through 32 removed outlier: 3.518A pdb=" N ALA o 32 " --> pdb=" O LYS o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 50 removed outlier: 4.221A pdb=" N MET o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 55 No H-bonds generated for 'chain 'o' and resid 53 through 55' Processing helix chain 'o' and resid 57 through 59 No H-bonds generated for 'chain 'o' and resid 57 through 59' Processing helix chain 'o' and resid 81 through 89 Processing helix chain 't' and resid 13 through 23 Processing helix chain 't' and resid 42 through 44 No H-bonds generated for 'chain 't' and resid 42 through 44' Processing helix chain 't' and resid 72 through 74 No H-bonds generated for 'chain 't' and resid 72 through 74' Processing sheet with id= A, first strand: chain 'd' and resid 101 through 105 removed outlier: 7.090A pdb=" N VAL d 66 " --> pdb=" O SER d 102 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASN d 104 " --> pdb=" O VAL d 66 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE d 68 " --> pdb=" O ASN d 104 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN d 54 " --> pdb=" O SER d 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'd' and resid 165 through 171 removed outlier: 3.841A pdb=" N GLY d 148 " --> pdb=" O PHE d 203 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'j' and resid 3 through 7 removed outlier: 6.632A pdb=" N LYS j 25 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE j 63 " --> pdb=" O LYS j 25 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL j 27 " --> pdb=" O ILE j 63 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'k' and resid 96 through 101 removed outlier: 4.241A pdb=" N LYS k 71 " --> pdb=" O MET k 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'k' and resid 45 through 52 Processing sheet with id= F, first strand: chain 't' and resid 31 through 33 249 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 596 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 7.83 Time building geometry restraints manager: 10.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2429 1.33 - 1.45: 7222 1.45 - 1.57: 7536 1.57 - 1.69: 950 1.69 - 1.82: 45 Bond restraints: 18182 Sorted by residual: bond pdb=" C8 T1C 31624 " pdb=" C9 T1C 31624 " ideal model delta sigma weight residual 1.024 1.393 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C12 T1C 31624 " pdb=" C1C T1C 31624 " ideal model delta sigma weight residual 1.155 1.506 -0.351 2.00e-02 2.50e+03 3.08e+02 bond pdb=" C41 T1C 31624 " pdb=" C5 T1C 31624 " ideal model delta sigma weight residual 1.852 1.524 0.328 2.00e-02 2.50e+03 2.68e+02 bond pdb=" C6 T1C 31624 " pdb=" C61 T1C 31624 " ideal model delta sigma weight residual 1.796 1.492 0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C11 T1C 31624 " pdb=" C1A T1C 31624 " ideal model delta sigma weight residual 1.207 1.455 -0.248 2.00e-02 2.50e+03 1.54e+02 ... (remaining 18177 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 2916 106.29 - 113.23: 10405 113.23 - 120.17: 6713 120.17 - 127.11: 5749 127.11 - 134.05: 1101 Bond angle restraints: 26884 Sorted by residual: angle pdb=" C1A T1C 31624 " pdb=" C61 T1C 31624 " pdb=" C7 T1C 31624 " ideal model delta sigma weight residual 105.85 120.30 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C10 T1C 31624 " pdb=" C1A T1C 31624 " pdb=" C61 T1C 31624 " ideal model delta sigma weight residual 105.73 119.14 -13.41 3.00e+00 1.11e-01 2.00e+01 angle pdb=" C2' A 3 955 " pdb=" C1' A 3 955 " pdb=" N9 A 3 955 " ideal model delta sigma weight residual 112.00 118.03 -6.03 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C41 T1C 31624 " pdb=" C5 T1C 31624 " pdb=" C51 T1C 31624 " ideal model delta sigma weight residual 100.12 112.06 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C11 T1C 31624 " pdb=" C1A T1C 31624 " pdb=" C61 T1C 31624 " ideal model delta sigma weight residual 130.35 119.66 10.69 3.00e+00 1.11e-01 1.27e+01 ... (remaining 26879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 10120 34.06 - 68.11: 1352 68.11 - 102.17: 150 102.17 - 136.22: 1 136.22 - 170.28: 9 Dihedral angle restraints: 11632 sinusoidal: 9196 harmonic: 2436 Sorted by residual: dihedral pdb=" O4' C 3 964 " pdb=" C1' C 3 964 " pdb=" N1 C 3 964 " pdb=" C2 C 3 964 " ideal model delta sinusoidal sigma weight residual 200.00 38.70 161.30 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" O4' C 31155 " pdb=" C1' C 31155 " pdb=" N1 C 31155 " pdb=" C2 C 31155 " ideal model delta sinusoidal sigma weight residual 200.00 49.08 150.92 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U 3 957 " pdb=" C1' U 3 957 " pdb=" N1 U 3 957 " pdb=" C2 U 3 957 " ideal model delta sinusoidal sigma weight residual 232.00 61.72 170.28 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 11629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3306 0.120 - 0.240: 108 0.240 - 0.360: 1 0.360 - 0.480: 1 0.480 - 0.600: 1 Chirality restraints: 3417 Sorted by residual: chirality pdb=" C41 T1C 31624 " pdb=" C1C T1C 31624 " pdb=" C4 T1C 31624 " pdb=" C5 T1C 31624 " both_signs ideal model delta sigma weight residual False 3.12 2.52 0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" C4 T1C 31624 " pdb=" C3 T1C 31624 " pdb=" C41 T1C 31624 " pdb=" N4 T1C 31624 " both_signs ideal model delta sigma weight residual False 2.59 2.12 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C1' U 31080 " pdb=" O4' U 31080 " pdb=" C2' U 31080 " pdb=" N1 U 31080 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 3414 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C9 T1C 31624 " -0.194 2.00e-02 2.50e+03 1.62e-01 3.28e+02 pdb=" C91 T1C 31624 " 0.054 2.00e-02 2.50e+03 pdb=" C92 T1C 31624 " -0.132 2.00e-02 2.50e+03 pdb=" N9 T1C 31624 " 0.271 2.00e-02 2.50e+03 pdb=" O91 T1C 31624 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 3 955 " -0.052 2.00e-02 2.50e+03 2.36e-02 1.53e+01 pdb=" N9 A 3 955 " 0.053 2.00e-02 2.50e+03 pdb=" C8 A 3 955 " 0.009 2.00e-02 2.50e+03 pdb=" N7 A 3 955 " -0.006 2.00e-02 2.50e+03 pdb=" C5 A 3 955 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 3 955 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A 3 955 " -0.012 2.00e-02 2.50e+03 pdb=" N1 A 3 955 " -0.009 2.00e-02 2.50e+03 pdb=" C2 A 3 955 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A 3 955 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 3 955 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 31219 " -0.047 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" N9 G 31219 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G 31219 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G 31219 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G 31219 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 31219 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G 31219 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 31219 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G 31219 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 31219 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G 31219 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G 31219 " -0.001 2.00e-02 2.50e+03 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 154 2.50 - 3.10: 11466 3.10 - 3.70: 31842 3.70 - 4.30: 46951 4.30 - 4.90: 64224 Nonbonded interactions: 154637 Sorted by model distance: nonbonded pdb=" OP1 G 31091 " pdb="MG MG 31616 " model vdw 1.898 2.170 nonbonded pdb=" OP2 G 31091 " pdb="MG MG 31616 " model vdw 1.909 2.170 nonbonded pdb=" O6 G 31105 " pdb="MG MG 31608 " model vdw 1.953 2.170 nonbonded pdb=" OP1 C 3 977 " pdb="MG MG 31613 " model vdw 1.973 2.170 nonbonded pdb=" OP2 U 31092 " pdb="MG MG 31608 " model vdw 1.983 2.170 ... (remaining 154632 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: 2.440 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: 13.160 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 56.860 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.369 18182 Z= 0.722 Angle : 0.918 14.451 26884 Z= 0.475 Chirality : 0.051 0.600 3417 Planarity : 0.007 0.162 1651 Dihedral : 24.042 170.278 10058 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.73 % Favored : 91.03 % Rotamer: Outliers : 11.09 % Allowed : 32.12 % Favored : 56.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.10 (0.24), residues: 836 helix: -3.22 (0.19), residues: 344 sheet: -0.70 (0.44), residues: 133 loop : -2.89 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP d 22 HIS 0.007 0.002 HIS k 15 PHE 0.023 0.003 PHE n 23 TYR 0.017 0.003 TYR t 80 ARG 0.006 0.001 ARG j 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 182 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 58 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6183 (mt-10) REVERT: h 53 LYS cc_start: 0.7225 (tttm) cc_final: 0.6803 (ptpp) REVERT: k 14 ASP cc_start: 0.5082 (t70) cc_final: 0.4196 (t70) REVERT: k 85 ASP cc_start: 0.3669 (OUTLIER) cc_final: 0.3431 (p0) REVERT: n 76 ASN cc_start: 0.6346 (OUTLIER) cc_final: 0.5284 (m-40) REVERT: n 79 ARG cc_start: 0.6974 (ttm110) cc_final: 0.6616 (ttt-90) REVERT: o 73 TYR cc_start: 0.7373 (t80) cc_final: 0.7118 (t80) REVERT: t 35 SER cc_start: 0.6216 (OUTLIER) cc_final: 0.5988 (t) outliers start: 76 outliers final: 35 residues processed: 242 average time/residue: 1.4202 time to fit residues: 380.2637 Evaluate side-chains 192 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 153 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 66 LYS Chi-restraints excluded: chain j residue 97 ARG Chi-restraints excluded: chain j residue 98 GLN Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 45 ILE Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 76 ASN Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 35 SER Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 50 SER Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 3 GLN d 6 HIS d 21 ASN d 28 GLN d 88 GLN d 93 ASN d 140 ASN h 21 GLN h 51 GLN j 73 GLN j 79 HIS k 35 GLN k 58 ASN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 71 HIS t 14 HIS ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18182 Z= 0.187 Angle : 0.655 15.595 26884 Z= 0.326 Chirality : 0.039 0.344 3417 Planarity : 0.005 0.052 1651 Dihedral : 23.551 170.278 8464 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.94 % Favored : 92.94 % Rotamer: Outliers : 9.93 % Allowed : 34.74 % Favored : 55.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.34 (0.27), residues: 836 helix: -1.65 (0.24), residues: 347 sheet: 0.22 (0.47), residues: 132 loop : -2.05 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 201 HIS 0.004 0.001 HIS d 6 PHE 0.018 0.002 PHE n 23 TYR 0.010 0.002 TYR n 86 ARG 0.005 0.000 ARG n 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 165 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 53 LYS cc_start: 0.6933 (tttm) cc_final: 0.6634 (ptpp) REVERT: j 105 ASP cc_start: 0.7173 (t0) cc_final: 0.6707 (t70) REVERT: k 85 ASP cc_start: 0.3930 (OUTLIER) cc_final: 0.3687 (p0) REVERT: n 79 ARG cc_start: 0.6916 (ttm110) cc_final: 0.6620 (ttt-90) REVERT: o 10 GLU cc_start: 0.5605 (OUTLIER) cc_final: 0.5164 (tt0) REVERT: o 73 TYR cc_start: 0.7331 (t80) cc_final: 0.7032 (t80) outliers start: 68 outliers final: 28 residues processed: 211 average time/residue: 1.3654 time to fit residues: 318.7855 Evaluate side-chains 181 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 129 MET Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 97 ARG Chi-restraints excluded: chain j residue 108 GLU Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 26 ASN Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 50 SER Chi-restraints excluded: chain t residue 55 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 28 GLN d 88 GLN d 140 ASN h 51 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18182 Z= 0.158 Angle : 0.606 13.792 26884 Z= 0.300 Chirality : 0.036 0.305 3417 Planarity : 0.004 0.046 1651 Dihedral : 23.224 171.692 8422 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 7.74 % Allowed : 37.23 % Favored : 55.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.16 (0.29), residues: 836 helix: -0.42 (0.28), residues: 331 sheet: 0.68 (0.48), residues: 136 loop : -1.62 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 201 HIS 0.003 0.001 HIS k 15 PHE 0.015 0.001 PHE n 23 TYR 0.010 0.002 TYR n 86 ARG 0.004 0.000 ARG t 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 161 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 83 ASP cc_start: 0.4169 (t0) cc_final: 0.3860 (t0) REVERT: d 104 ASN cc_start: 0.5841 (OUTLIER) cc_final: 0.5069 (m110) REVERT: h 53 LYS cc_start: 0.7002 (tttm) cc_final: 0.6731 (ptpp) REVERT: j 105 ASP cc_start: 0.6978 (t0) cc_final: 0.6540 (t70) REVERT: k 47 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: n 75 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.5336 (ttp) REVERT: n 79 ARG cc_start: 0.6959 (ttm110) cc_final: 0.6725 (ttt-90) REVERT: o 10 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.5230 (tt0) REVERT: o 73 TYR cc_start: 0.7308 (t80) cc_final: 0.6994 (t80) outliers start: 53 outliers final: 20 residues processed: 196 average time/residue: 1.2156 time to fit residues: 266.8696 Evaluate side-chains 166 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 104 ASN Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 129 MET Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 14 ASP Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 55 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 125 optimal weight: 0.0570 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 88 GLN ** d 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 51 GLN j 35 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18182 Z= 0.235 Angle : 0.677 13.610 26884 Z= 0.333 Chirality : 0.039 0.320 3417 Planarity : 0.005 0.047 1651 Dihedral : 23.205 169.936 8403 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.42 % Favored : 92.46 % Rotamer: Outliers : 9.34 % Allowed : 35.77 % Favored : 54.89 % 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: -1.04 (0.29), residues: 836 helix: -0.32 (0.28), residues: 337 sheet: 0.59 (0.47), residues: 140 loop : -1.52 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP d 201 HIS 0.005 0.001 HIS k 15 PHE 0.014 0.002 PHE h 18 TYR 0.014 0.002 TYR d 29 ARG 0.004 0.000 ARG h 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 146 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 104 ASN cc_start: 0.5920 (OUTLIER) cc_final: 0.5156 (m110) REVERT: d 112 ASP cc_start: 0.5705 (OUTLIER) cc_final: 0.5458 (m-30) REVERT: d 127 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6130 (mpt180) REVERT: d 164 ARG cc_start: 0.6774 (mtm180) cc_final: 0.6556 (mtp85) REVERT: h 53 LYS cc_start: 0.7169 (tttm) cc_final: 0.6834 (ptpp) REVERT: j 105 ASP cc_start: 0.7093 (t0) cc_final: 0.6637 (t70) REVERT: k 47 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6590 (pt0) REVERT: n 75 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.5342 (ttp) REVERT: n 79 ARG cc_start: 0.6983 (ttm110) cc_final: 0.6569 (ttt-90) REVERT: n 98 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6329 (mpt-90) REVERT: o 10 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.5210 (tt0) REVERT: o 61 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7265 (ttt90) REVERT: o 73 TYR cc_start: 0.7357 (t80) cc_final: 0.7065 (t80) REVERT: o 76 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6599 (tptt) REVERT: t 20 GLU cc_start: 0.4296 (OUTLIER) cc_final: 0.3982 (pp20) outliers start: 64 outliers final: 32 residues processed: 189 average time/residue: 1.3086 time to fit residues: 274.8785 Evaluate side-chains 181 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 104 ASN Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 127 ARG Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 97 ARG Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 14 ASP Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 98 ARG Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 92 ASP Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 107 optimal weight: 0.0770 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 88 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18182 Z= 0.189 Angle : 0.632 13.430 26884 Z= 0.313 Chirality : 0.037 0.326 3417 Planarity : 0.004 0.046 1651 Dihedral : 23.123 170.792 8399 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Rotamer: Outliers : 8.76 % Allowed : 37.37 % Favored : 53.87 % 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: -0.73 (0.30), residues: 836 helix: -0.00 (0.29), residues: 331 sheet: 0.66 (0.47), residues: 140 loop : -1.36 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP d 201 HIS 0.004 0.001 HIS k 15 PHE 0.011 0.002 PHE h 18 TYR 0.011 0.002 TYR d 29 ARG 0.005 0.000 ARG h 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 145 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 104 ASN cc_start: 0.5908 (OUTLIER) cc_final: 0.5134 (m110) REVERT: h 53 LYS cc_start: 0.7116 (tttm) cc_final: 0.6673 (ptpp) REVERT: h 114 LYS cc_start: 0.4478 (OUTLIER) cc_final: 0.3887 (mmtt) REVERT: j 105 ASP cc_start: 0.7183 (t0) cc_final: 0.6704 (t70) REVERT: k 47 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6492 (pt0) REVERT: n 75 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.5230 (ttp) REVERT: n 79 ARG cc_start: 0.6987 (ttm110) cc_final: 0.6733 (ttt-90) REVERT: n 98 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6352 (mpt-90) REVERT: o 10 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5314 (tt0) REVERT: o 61 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7188 (ttt90) REVERT: o 73 TYR cc_start: 0.7330 (t80) cc_final: 0.7040 (t80) REVERT: o 76 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6583 (tptt) REVERT: t 20 GLU cc_start: 0.4153 (OUTLIER) cc_final: 0.3888 (pp20) outliers start: 60 outliers final: 35 residues processed: 190 average time/residue: 1.2849 time to fit residues: 271.1860 Evaluate side-chains 185 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 87 LEU Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 104 ASN Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 129 MET Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 114 LYS Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 97 ARG Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 14 ASP Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 66 GLU Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 98 ARG Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 139 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18182 Z= 0.195 Angle : 0.637 13.238 26884 Z= 0.314 Chirality : 0.036 0.332 3417 Planarity : 0.004 0.043 1651 Dihedral : 23.074 170.753 8399 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Rotamer: Outliers : 9.20 % Allowed : 37.52 % Favored : 53.28 % 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: -0.60 (0.30), residues: 836 helix: 0.12 (0.29), residues: 330 sheet: 0.68 (0.47), residues: 140 loop : -1.27 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP d 201 HIS 0.003 0.001 HIS k 15 PHE 0.011 0.001 PHE d 130 TYR 0.011 0.002 TYR d 29 ARG 0.007 0.000 ARG h 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 150 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 104 ASN cc_start: 0.5909 (OUTLIER) cc_final: 0.5120 (m110) REVERT: h 53 LYS cc_start: 0.7090 (tttm) cc_final: 0.6766 (ptpp) REVERT: j 105 ASP cc_start: 0.7167 (t0) cc_final: 0.6695 (t70) REVERT: k 47 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6484 (pt0) REVERT: n 75 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.5198 (ttp) REVERT: n 79 ARG cc_start: 0.7015 (ttm110) cc_final: 0.6749 (ttt-90) REVERT: n 98 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6353 (mpt-90) REVERT: o 10 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5314 (tt0) REVERT: o 61 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7207 (ttt90) REVERT: o 73 TYR cc_start: 0.7338 (t80) cc_final: 0.7045 (t80) REVERT: o 76 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6585 (tptt) REVERT: t 20 GLU cc_start: 0.4285 (OUTLIER) cc_final: 0.3975 (pp20) outliers start: 63 outliers final: 39 residues processed: 198 average time/residue: 1.2605 time to fit residues: 278.3515 Evaluate side-chains 188 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 141 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 87 LEU Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 104 ASN Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 129 MET Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 97 ARG Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 66 GLU Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 98 ARG Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 57 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 52 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 18182 Z= 0.156 Angle : 0.599 12.976 26884 Z= 0.296 Chirality : 0.035 0.331 3417 Planarity : 0.004 0.043 1651 Dihedral : 22.991 172.230 8399 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 7.15 % Allowed : 38.83 % Favored : 54.01 % 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: -0.40 (0.30), residues: 836 helix: 0.28 (0.29), residues: 332 sheet: 0.73 (0.46), residues: 141 loop : -1.15 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 201 HIS 0.003 0.001 HIS k 15 PHE 0.011 0.001 PHE h 61 TYR 0.009 0.001 TYR d 29 ARG 0.011 0.000 ARG h 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 154 SER cc_start: 0.7999 (t) cc_final: 0.7765 (m) REVERT: h 53 LYS cc_start: 0.7038 (tttm) cc_final: 0.6705 (ptpp) REVERT: j 105 ASP cc_start: 0.7073 (t0) cc_final: 0.6621 (t70) REVERT: k 88 MET cc_start: 0.5364 (mmt) cc_final: 0.4569 (ppp) REVERT: n 75 MET cc_start: 0.5445 (OUTLIER) cc_final: 0.5117 (ttp) REVERT: n 79 ARG cc_start: 0.6976 (ttm110) cc_final: 0.6686 (ttt-90) REVERT: n 98 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6440 (mpt-90) REVERT: o 10 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5240 (tt0) REVERT: o 73 TYR cc_start: 0.7303 (t80) cc_final: 0.7000 (t80) REVERT: o 76 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6434 (tptt) REVERT: t 55 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5819 (ptp-170) outliers start: 49 outliers final: 25 residues processed: 192 average time/residue: 1.2638 time to fit residues: 270.6166 Evaluate side-chains 178 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 129 MET Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 14 ASP Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 98 ARG Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 88 GLN d 140 ASN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 18182 Z= 0.343 Angle : 0.784 13.423 26884 Z= 0.383 Chirality : 0.043 0.365 3417 Planarity : 0.006 0.083 1651 Dihedral : 23.144 171.326 8397 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.66 % Favored : 92.11 % Rotamer: Outliers : 8.03 % Allowed : 38.98 % Favored : 52.99 % 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: -0.80 (0.29), residues: 836 helix: -0.20 (0.29), residues: 324 sheet: 0.66 (0.47), residues: 140 loop : -1.24 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP t 34 HIS 0.005 0.001 HIS k 15 PHE 0.018 0.003 PHE d 130 TYR 0.018 0.003 TYR d 184 ARG 0.006 0.001 ARG h 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 151 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: d 112 ASP cc_start: 0.5823 (OUTLIER) cc_final: 0.5580 (m-30) REVERT: d 154 SER cc_start: 0.8052 (t) cc_final: 0.7837 (m) REVERT: h 53 LYS cc_start: 0.7196 (tttm) cc_final: 0.6687 (ptpp) REVERT: j 105 ASP cc_start: 0.7208 (t0) cc_final: 0.6726 (t70) REVERT: n 75 MET cc_start: 0.5589 (tmm) cc_final: 0.5270 (ttp) REVERT: n 79 ARG cc_start: 0.7048 (ttm110) cc_final: 0.6586 (ttt-90) REVERT: n 98 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6395 (mpt-90) REVERT: o 10 GLU cc_start: 0.5568 (OUTLIER) cc_final: 0.5023 (tt0) REVERT: o 61 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7262 (ttt90) REVERT: o 73 TYR cc_start: 0.7366 (t80) cc_final: 0.7075 (t80) REVERT: o 76 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6784 (tptt) REVERT: t 20 GLU cc_start: 0.4273 (OUTLIER) cc_final: 0.3954 (pp20) REVERT: t 55 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5915 (ptp-170) outliers start: 55 outliers final: 32 residues processed: 192 average time/residue: 1.2898 time to fit residues: 275.2417 Evaluate side-chains 185 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 129 MET Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 184 TYR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 14 ASP Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 98 ARG Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 51 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18182 Z= 0.302 Angle : 0.755 13.592 26884 Z= 0.371 Chirality : 0.042 0.378 3417 Planarity : 0.006 0.074 1651 Dihedral : 23.147 171.187 8397 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.30 % Favored : 92.46 % Rotamer: Outliers : 7.74 % Allowed : 40.00 % Favored : 52.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.96 (0.29), residues: 836 helix: -0.37 (0.28), residues: 323 sheet: 0.54 (0.47), residues: 140 loop : -1.28 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP t 34 HIS 0.005 0.001 HIS k 15 PHE 0.040 0.003 PHE d 203 TYR 0.014 0.002 TYR d 29 ARG 0.005 0.001 ARG n 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 144 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 112 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.5589 (m-30) REVERT: d 154 SER cc_start: 0.8110 (t) cc_final: 0.7854 (m) REVERT: h 53 LYS cc_start: 0.7247 (tttm) cc_final: 0.6694 (ptpp) REVERT: j 105 ASP cc_start: 0.7182 (t0) cc_final: 0.6722 (t70) REVERT: n 75 MET cc_start: 0.5582 (tmm) cc_final: 0.5281 (ttp) REVERT: n 79 ARG cc_start: 0.6894 (ttm110) cc_final: 0.6488 (ttt-90) REVERT: o 10 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.4972 (tt0) REVERT: o 61 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7244 (ttt90) REVERT: o 73 TYR cc_start: 0.7305 (t80) cc_final: 0.7011 (t80) REVERT: o 76 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6626 (tptt) REVERT: t 20 GLU cc_start: 0.4281 (OUTLIER) cc_final: 0.3978 (pp20) REVERT: t 55 ARG cc_start: 0.6240 (OUTLIER) cc_final: 0.5873 (ptp-170) outliers start: 53 outliers final: 35 residues processed: 184 average time/residue: 1.2396 time to fit residues: 254.2549 Evaluate side-chains 184 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 67 THR Chi-restraints excluded: chain d residue 68 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 129 MET Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 28 ILE Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 91 ASP Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 51 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18182 Z= 0.175 Angle : 0.638 13.182 26884 Z= 0.317 Chirality : 0.036 0.359 3417 Planarity : 0.005 0.070 1651 Dihedral : 23.015 171.905 8397 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.46 % Favored : 93.42 % Rotamer: Outliers : 5.84 % Allowed : 41.90 % Favored : 52.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.30), residues: 836 helix: 0.03 (0.30), residues: 325 sheet: 0.79 (0.47), residues: 139 loop : -1.13 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 201 HIS 0.004 0.001 HIS t 52 PHE 0.021 0.002 PHE d 203 TYR 0.009 0.001 TYR d 29 ARG 0.006 0.000 ARG n 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 204 ARG cc_start: 0.6614 (mtm180) cc_final: 0.6311 (mtt90) REVERT: h 53 LYS cc_start: 0.7258 (tttm) cc_final: 0.6748 (ptpp) REVERT: j 105 ASP cc_start: 0.7092 (t0) cc_final: 0.6637 (t70) REVERT: n 75 MET cc_start: 0.5466 (tmm) cc_final: 0.5120 (ttp) REVERT: n 79 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6512 (ttt-90) REVERT: o 10 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5269 (tt0) REVERT: o 61 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7164 (ttt90) REVERT: o 73 TYR cc_start: 0.7312 (t80) cc_final: 0.7035 (t80) REVERT: o 76 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6530 (tptt) REVERT: t 20 GLU cc_start: 0.4214 (OUTLIER) cc_final: 0.3895 (pp20) REVERT: t 55 ARG cc_start: 0.5915 (OUTLIER) cc_final: 0.5551 (ptp-170) outliers start: 40 outliers final: 28 residues processed: 175 average time/residue: 1.2978 time to fit residues: 253.2557 Evaluate side-chains 170 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 112 ASP Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 129 MET Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 51 GLN Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 64 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 126 SER Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 10 GLU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 76 LYS Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain t residue 20 GLU Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 55 ARG Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 51 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.178171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.156699 restraints weight = 22707.554| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 0.88 r_work: 0.3915 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18182 Z= 0.302 Angle : 0.759 14.470 26884 Z= 0.372 Chirality : 0.041 0.366 3417 Planarity : 0.006 0.071 1651 Dihedral : 23.081 170.839 8396 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.01 % Favored : 91.75 % Rotamer: Outliers : 6.13 % Allowed : 41.90 % Favored : 51.97 % 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: -0.82 (0.29), residues: 836 helix: -0.28 (0.28), residues: 324 sheet: 0.63 (0.47), residues: 140 loop : -1.17 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP t 34 HIS 0.005 0.001 HIS k 15 PHE 0.041 0.003 PHE d 203 TYR 0.015 0.002 TYR d 184 ARG 0.005 0.001 ARG h 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5150.14 seconds wall clock time: 93 minutes 26.18 seconds (5606.18 seconds total)