Starting phenix.real_space_refine (version: dev) on Wed Dec 14 02:10:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/12_2022/7afk_11768_neut_updated.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18521 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 35, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 170} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.74, per 1000 atoms: 0.58 Number of scatterers: 18521 At special positions: 0 Unit cell: (118.265, 116.095, 159.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 12 11.99 O 4730 8.00 N 3449 7.00 C 9845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.77 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 10 sheets defined 42.2% alpha, 11.9% beta 116 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 9.48 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.674A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 30 through 49 removed outlier: 5.977A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 95 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.573A pdb=" N ALA G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 4.284A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.516A pdb=" N SER G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 147 removed outlier: 3.613A pdb=" N ALA G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA G 147 " --> pdb=" O ARG G 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 95 through 101 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 88 removed outlier: 4.240A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 4.582A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 removed outlier: 4.405A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 40 through 50 Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.898A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.696A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.928A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 54 through 58 Processing sheet with id= D, first strand: chain 'C' and resid 165 through 171 Processing sheet with id= E, first strand: chain 'G' and resid 73 through 75 Processing sheet with id= F, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= G, first strand: chain 'I' and resid 21 through 23 Processing sheet with id= H, first strand: chain 'J' and resid 70 through 76 Processing sheet with id= I, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= J, first strand: chain 'S' and resid 31 through 33 removed outlier: 4.056A pdb=" N LEU S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 8.65 Time building geometry restraints manager: 13.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2828 1.33 - 1.45: 7327 1.45 - 1.57: 8682 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19801 Sorted by residual: bond pdb=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.500 1.343 0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.500 1.353 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C2 5MC 1 967 " pdb=" N3 5MC 1 967 " ideal model delta sigma weight residual 1.492 1.351 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.481 1.340 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C2 2MG 1 966 " pdb=" N2 2MG 1 966 " ideal model delta sigma weight residual 1.481 1.349 0.132 2.00e-02 2.50e+03 4.36e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.93: 2994 106.93 - 114.27: 12253 114.27 - 121.61: 9175 121.61 - 128.95: 3982 128.95 - 136.29: 545 Bond angle restraints: 28949 Sorted by residual: angle pdb=" N SER I 93 " pdb=" CA SER I 93 " pdb=" C SER I 93 " ideal model delta sigma weight residual 113.88 105.93 7.95 1.23e+00 6.61e-01 4.18e+01 angle pdb=" O3' C 11103 " pdb=" C3' C 11103 " pdb=" C2' C 11103 " ideal model delta sigma weight residual 113.70 121.69 -7.99 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 109.53 125.29 -15.76 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O3' A 11157 " pdb=" C3' A 11157 " pdb=" C2' A 11157 " ideal model delta sigma weight residual 109.50 101.96 7.54 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 109.53 124.30 -14.77 3.00e+00 1.11e-01 2.42e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 10349 35.78 - 71.56: 561 71.56 - 107.34: 64 107.34 - 143.12: 4 143.12 - 178.90: 4 Dihedral angle restraints: 10982 sinusoidal: 7812 harmonic: 3170 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual 200.00 33.90 166.10 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual -128.00 50.90 -178.90 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 232.00 54.69 177.31 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 10979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3181 0.077 - 0.154: 328 0.154 - 0.231: 77 0.231 - 0.308: 9 0.308 - 0.385: 2 Chirality restraints: 3597 Sorted by residual: chirality pdb=" C3' C 11103 " pdb=" C4' C 11103 " pdb=" O3' C 11103 " pdb=" C2' C 11103 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE J 49 " pdb=" N PHE J 49 " pdb=" C PHE J 49 " pdb=" CB PHE J 49 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' A 1 969 " pdb=" C4' A 1 969 " pdb=" O3' A 1 969 " pdb=" C2' A 1 969 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3594 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " -0.060 2.00e-02 2.50e+03 6.06e-01 8.25e+03 pdb=" C4' 2MG 11207 " -0.456 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " -0.652 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " 0.645 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " 0.178 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " -0.967 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " -0.219 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " 0.943 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " -0.244 2.00e-02 2.50e+03 4.30e-01 4.16e+03 pdb=" C4' 2MG 1 966 " 0.408 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " 0.602 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " -0.481 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " -0.131 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " -0.346 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " 0.478 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " 0.324 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " -0.610 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " 0.297 2.00e-02 2.50e+03 3.72e-01 3.11e+03 pdb=" C4' 5MC 1 967 " -0.378 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " -0.499 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " 0.444 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " -0.056 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " 0.396 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " -0.315 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " -0.332 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " 0.443 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 55 2.20 - 2.87: 7458 2.87 - 3.55: 35181 3.55 - 4.22: 60195 4.22 - 4.90: 80339 Nonbonded interactions: 183228 Sorted by model distance: nonbonded pdb=" O3' U 1 952 " pdb="MG MG 11608 " model vdw 1.519 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11610 " model vdw 1.629 2.170 nonbonded pdb=" OP1 A 1 964 " pdb="MG MG 11611 " model vdw 1.659 2.170 nonbonded pdb=" OP2 C 1 972 " pdb="MG MG 11607 " model vdw 1.697 2.170 nonbonded pdb=" OP1 C 11109 " pdb="MG MG 11604 " model vdw 1.732 2.170 ... (remaining 183223 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 12 5.21 5 S 28 5.16 5 C 9845 2.51 5 N 3449 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 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: 13.260 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.150 Process input model: 66.920 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.157 19801 Z= 0.476 Angle : 0.884 15.763 28949 Z= 0.550 Chirality : 0.053 0.385 3597 Planarity : 0.019 0.606 1998 Dihedral : 18.395 178.902 8930 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 42.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1092 helix: -1.23 (0.22), residues: 480 sheet: -2.30 (0.36), residues: 161 loop : -2.40 (0.27), residues: 451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3547 time to fit residues: 122.6866 Evaluate side-chains 145 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 0.0050 chunk 39 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 227 GLN C 140 ASN G 122 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19801 Z= 0.211 Angle : 0.729 14.348 28949 Z= 0.396 Chirality : 0.038 0.248 3597 Planarity : 0.007 0.119 1998 Dihedral : 18.310 179.262 6705 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 34.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.24), residues: 1092 helix: -0.22 (0.23), residues: 488 sheet: -1.80 (0.36), residues: 153 loop : -1.84 (0.28), residues: 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.3411 time to fit residues: 94.9445 Evaluate side-chains 131 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 19801 Z= 0.218 Angle : 0.687 13.918 28949 Z= 0.376 Chirality : 0.036 0.265 3597 Planarity : 0.007 0.123 1998 Dihedral : 18.148 179.354 6705 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 33.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.00 % 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: -1.36 (0.24), residues: 1092 helix: 0.04 (0.23), residues: 487 sheet: -1.53 (0.37), residues: 158 loop : -1.63 (0.28), residues: 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3486 time to fit residues: 91.8432 Evaluate side-chains 131 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 19801 Z= 0.308 Angle : 0.752 13.575 28949 Z= 0.406 Chirality : 0.038 0.252 3597 Planarity : 0.007 0.125 1998 Dihedral : 18.456 177.186 6705 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 42.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 0.00 % 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: -1.36 (0.24), residues: 1092 helix: -0.01 (0.23), residues: 492 sheet: -1.48 (0.37), residues: 158 loop : -1.61 (0.28), residues: 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3306 time to fit residues: 83.4108 Evaluate side-chains 130 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19801 Z= 0.197 Angle : 0.679 13.514 28949 Z= 0.372 Chirality : 0.036 0.255 3597 Planarity : 0.006 0.121 1998 Dihedral : 18.087 179.761 6705 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 32.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.00 % 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: -1.11 (0.25), residues: 1092 helix: 0.25 (0.23), residues: 489 sheet: -1.24 (0.38), residues: 159 loop : -1.60 (0.29), residues: 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3157 time to fit residues: 76.6646 Evaluate side-chains 126 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 122 optimal weight: 0.0670 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 overall best weight: 7.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 19801 Z= 0.419 Angle : 0.846 13.235 28949 Z= 0.447 Chirality : 0.042 0.250 3597 Planarity : 0.008 0.128 1998 Dihedral : 18.707 176.680 6705 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 50.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.00 % 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 (0.24), residues: 1092 helix: -0.24 (0.23), residues: 489 sheet: -1.62 (0.36), residues: 163 loop : -1.83 (0.28), residues: 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3126 time to fit residues: 73.1966 Evaluate side-chains 116 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 147 optimal weight: 0.0970 chunk 92 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19801 Z= 0.200 Angle : 0.690 13.268 28949 Z= 0.378 Chirality : 0.036 0.282 3597 Planarity : 0.007 0.121 1998 Dihedral : 18.202 179.416 6705 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 33.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1092 helix: 0.21 (0.23), residues: 485 sheet: -1.23 (0.38), residues: 161 loop : -1.70 (0.27), residues: 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3269 time to fit residues: 80.5892 Evaluate side-chains 121 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 19801 Z= 0.426 Angle : 0.860 13.031 28949 Z= 0.453 Chirality : 0.043 0.275 3597 Planarity : 0.008 0.127 1998 Dihedral : 18.748 177.311 6705 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 51.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer Outliers : 0.00 % 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: -1.72 (0.24), residues: 1092 helix: -0.29 (0.22), residues: 485 sheet: -1.45 (0.38), residues: 164 loop : -1.89 (0.27), residues: 443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3557 time to fit residues: 76.3713 Evaluate side-chains 107 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 124 optimal weight: 0.0010 chunk 129 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19801 Z= 0.212 Angle : 0.702 13.396 28949 Z= 0.384 Chirality : 0.037 0.362 3597 Planarity : 0.007 0.120 1998 Dihedral : 18.179 178.293 6705 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 33.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.00 % 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: -1.22 (0.25), residues: 1092 helix: 0.16 (0.23), residues: 481 sheet: -1.29 (0.38), residues: 171 loop : -1.63 (0.28), residues: 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3230 time to fit residues: 77.8514 Evaluate side-chains 120 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 19801 Z= 0.250 Angle : 0.718 13.415 28949 Z= 0.390 Chirality : 0.037 0.273 3597 Planarity : 0.007 0.122 1998 Dihedral : 18.201 179.648 6705 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 36.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.00 % 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: -1.11 (0.25), residues: 1092 helix: 0.22 (0.24), residues: 476 sheet: -1.22 (0.38), residues: 164 loop : -1.50 (0.29), residues: 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.3077 time to fit residues: 70.3806 Evaluate side-chains 118 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.030590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.022430 restraints weight = 271590.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.023117 restraints weight = 155428.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.023476 restraints weight = 110104.316| |-----------------------------------------------------------------------------| r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 19801 Z= 0.357 Angle : 0.809 13.313 28949 Z= 0.431 Chirality : 0.040 0.275 3597 Planarity : 0.007 0.125 1998 Dihedral : 18.563 177.798 6705 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 46.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.52 (0.24), residues: 1092 helix: -0.11 (0.23), residues: 481 sheet: -1.50 (0.37), residues: 166 loop : -1.71 (0.28), residues: 445 =============================================================================== Job complete usr+sys time: 2776.07 seconds wall clock time: 53 minutes 17.35 seconds (3197.35 seconds total)