Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 06:48:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/04_2023/7ajq_11806.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/04_2023/7ajq_11806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/04_2023/7ajq_11806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/04_2023/7ajq_11806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/04_2023/7ajq_11806.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/04_2023/7ajq_11806.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.074 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 5817 2.51 5 N 1675 2.21 5 O 1689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 25": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9210 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 225} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 177 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "G" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 196 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Time building chain proxies: 5.06, per 1000 atoms: 0.55 Number of scatterers: 9210 At special positions: 0 Unit cell: (84.293, 87.494, 133.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1689 8.00 N 1675 7.00 C 5817 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: 4.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 87.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 57 through 100 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.530A pdb=" N ALA A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 140 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 206 through 272 removed outlier: 4.633A pdb=" N GLY A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 4.246A pdb=" N ALA A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.509A pdb=" N HIS A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 100 Processing helix chain 'B' and resid 104 through 114 removed outlier: 4.395A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 136 Processing helix chain 'B' and resid 140 through 164 Processing helix chain 'B' and resid 165 through 199 removed outlier: 4.107A pdb=" N PHE B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 206 through 280 removed outlier: 4.098A pdb=" N GLY B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 4.524A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 4.207A pdb=" N TYR C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 100 Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 119 through 135 Processing helix chain 'C' and resid 140 through 164 removed outlier: 3.608A pdb=" N ILE C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 199 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 207 through 280 Proline residue: C 227 - end of helix removed outlier: 4.447A pdb=" N ALA C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 57 through 99 Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing helix chain 'D' and resid 104 through 114 removed outlier: 3.515A pdb=" N ASN D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 135 Processing helix chain 'D' and resid 140 through 164 Processing helix chain 'D' and resid 165 through 199 removed outlier: 4.232A pdb=" N PHE D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 207 through 272 removed outlier: 3.506A pdb=" N ILE D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.908A pdb=" N ALA D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.551A pdb=" N GLN D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 100 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 119 through 135 Processing helix chain 'E' and resid 140 through 164 Processing helix chain 'E' and resid 166 through 199 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 207 through 277 removed outlier: 3.945A pdb=" N ILE E 211 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'F' and resid 22 through 38 removed outlier: 4.068A pdb=" N VAL F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 38 removed outlier: 4.168A pdb=" N ASP G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3175 1.34 - 1.46: 1464 1.46 - 1.57: 4643 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 9340 Sorted by residual: bond pdb=" C THR F 21 " pdb=" N PRO F 22 " ideal model delta sigma weight residual 1.337 1.369 -0.033 9.80e-03 1.04e+04 1.11e+01 bond pdb=" C HIS E 276 " pdb=" O HIS E 276 " ideal model delta sigma weight residual 1.235 1.249 -0.014 1.43e-02 4.89e+03 1.00e+00 bond pdb=" CA ALA A 136 " pdb=" C ALA A 136 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.64e-01 bond pdb=" CA THR F 21 " pdb=" C THR F 21 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.14e-01 bond pdb=" C ALA F 38 " pdb=" N PRO F 39 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.33e-01 ... (remaining 9335 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.23: 200 107.23 - 113.94: 5490 113.94 - 120.64: 4086 120.64 - 127.35: 2804 127.35 - 134.06: 77 Bond angle restraints: 12657 Sorted by residual: angle pdb=" N THR G 21 " pdb=" CA THR G 21 " pdb=" C THR G 21 " ideal model delta sigma weight residual 109.81 116.15 -6.34 2.21e+00 2.05e-01 8.23e+00 angle pdb=" N THR F 21 " pdb=" CA THR F 21 " pdb=" C THR F 21 " ideal model delta sigma weight residual 109.81 116.10 -6.29 2.21e+00 2.05e-01 8.10e+00 angle pdb=" CA LEU B 278 " pdb=" CB LEU B 278 " pdb=" CG LEU B 278 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" N SER A 135 " pdb=" CA SER A 135 " pdb=" C SER A 135 " ideal model delta sigma weight residual 111.11 108.33 2.78 1.20e+00 6.94e-01 5.37e+00 angle pdb=" C ALA D 136 " pdb=" N GLU D 137 " pdb=" CA GLU D 137 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.20e+00 ... (remaining 12652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5113 17.43 - 34.86: 395 34.86 - 52.29: 69 52.29 - 69.72: 9 69.72 - 87.14: 8 Dihedral angle restraints: 5594 sinusoidal: 2118 harmonic: 3476 Sorted by residual: dihedral pdb=" CA LEU B 278 " pdb=" C LEU B 278 " pdb=" N ARG B 279 " pdb=" CA ARG B 279 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA HIS E 276 " pdb=" C HIS E 276 " pdb=" N GLN E 277 " pdb=" CA GLN E 277 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA THR G 21 " pdb=" C THR G 21 " pdb=" N PRO G 22 " pdb=" CA PRO G 22 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 935 0.025 - 0.051: 339 0.051 - 0.076: 164 0.076 - 0.102: 46 0.102 - 0.127: 18 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA THR F 21 " pdb=" N THR F 21 " pdb=" C THR F 21 " pdb=" CB THR F 21 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CB VAL A 223 " pdb=" CA VAL A 223 " pdb=" CG1 VAL A 223 " pdb=" CG2 VAL A 223 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CB VAL G 29 " pdb=" CA VAL G 29 " pdb=" CG1 VAL G 29 " pdb=" CG2 VAL G 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1499 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 274 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C HIS C 274 " -0.029 2.00e-02 2.50e+03 pdb=" O HIS C 274 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA C 275 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 33 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.38e+00 pdb=" C ILE G 33 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE G 33 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE G 34 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 248 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" CG ASP C 248 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP C 248 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP C 248 " -0.007 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1227 2.75 - 3.28: 10405 3.28 - 3.82: 16218 3.82 - 4.36: 17160 4.36 - 4.90: 28997 Nonbonded interactions: 74007 Sorted by model distance: nonbonded pdb=" OG1 THR E 185 " pdb=" OG1 THR E 218 " model vdw 2.208 2.440 nonbonded pdb=" O GLU D 268 " pdb=" OG SER D 272 " model vdw 2.226 2.440 nonbonded pdb=" OG SER B 104 " pdb=" OD1 ASP B 106 " model vdw 2.239 2.440 nonbonded pdb=" O ASP C 262 " pdb=" OG1 THR C 266 " model vdw 2.253 2.440 nonbonded pdb=" O ASN D 162 " pdb=" NH1 ARG D 165 " model vdw 2.263 2.520 ... (remaining 74002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 52 through 281) selection = (chain 'C' and resid 52 through 281) selection = (chain 'D' and resid 52 through 281) selection = (chain 'E' and resid 52 through 281) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 18 through 40) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 4.610 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 26.820 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.002 0.033 9340 Z= 0.146 Angle : 0.553 8.204 12657 Z= 0.315 Chirality : 0.035 0.127 1502 Planarity : 0.003 0.029 1642 Dihedral : 13.098 87.144 3348 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: -0.98 (0.22), residues: 1208 helix: -0.03 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -3.52 (0.36), residues: 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.028 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 outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2246 time to fit residues: 90.9829 Evaluate side-chains 215 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 108 optimal weight: 0.0170 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN C 96 GLN C 129 GLN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN D 242 HIS ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN E 273 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9340 Z= 0.194 Angle : 0.698 11.123 12657 Z= 0.347 Chirality : 0.041 0.222 1502 Planarity : 0.004 0.039 1642 Dihedral : 4.061 22.786 1320 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 1.93 % 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: 0.57 (0.24), residues: 1208 helix: 1.05 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -3.29 (0.39), residues: 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 1.118 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 outliers start: 18 outliers final: 9 residues processed: 258 average time/residue: 0.2088 time to fit residues: 74.2728 Evaluate side-chains 233 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0923 time to fit residues: 3.4234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 36 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN A 273 GLN B 257 GLN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9340 Z= 0.183 Angle : 0.714 12.259 12657 Z= 0.352 Chirality : 0.041 0.184 1502 Planarity : 0.003 0.023 1642 Dihedral : 4.098 22.333 1320 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1208 helix: 1.32 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -3.14 (0.40), residues: 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 239 time to evaluate : 1.107 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: 17 outliers final: 8 residues processed: 247 average time/residue: 0.2153 time to fit residues: 73.5415 Evaluate side-chains 214 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0945 time to fit residues: 2.8005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN E 257 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9340 Z= 0.195 Angle : 0.713 10.750 12657 Z= 0.353 Chirality : 0.043 0.249 1502 Planarity : 0.003 0.029 1642 Dihedral : 4.128 21.974 1320 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 2.25 % 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: 1.14 (0.25), residues: 1208 helix: 1.41 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -3.13 (0.40), residues: 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 227 time to evaluate : 1.303 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: 21 outliers final: 13 residues processed: 239 average time/residue: 0.2149 time to fit residues: 71.0272 Evaluate side-chains 220 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0886 time to fit residues: 3.5697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9340 Z= 0.182 Angle : 0.753 12.486 12657 Z= 0.370 Chirality : 0.043 0.209 1502 Planarity : 0.003 0.029 1642 Dihedral : 4.163 21.490 1320 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1208 helix: 1.44 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -2.99 (0.41), residues: 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 225 time to evaluate : 1.146 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 outliers start: 11 outliers final: 6 residues processed: 233 average time/residue: 0.2084 time to fit residues: 67.4095 Evaluate side-chains 211 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0932 time to fit residues: 2.4396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9340 Z= 0.202 Angle : 0.757 12.864 12657 Z= 0.375 Chirality : 0.044 0.328 1502 Planarity : 0.003 0.033 1642 Dihedral : 4.210 21.641 1320 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.93 % 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: 1.19 (0.25), residues: 1208 helix: 1.42 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -2.88 (0.41), residues: 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 225 time to evaluate : 1.150 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: 18 outliers final: 7 residues processed: 235 average time/residue: 0.2145 time to fit residues: 69.7968 Evaluate side-chains 213 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1014 time to fit residues: 2.9940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9340 Z= 0.203 Angle : 0.807 13.107 12657 Z= 0.398 Chirality : 0.045 0.225 1502 Planarity : 0.004 0.075 1642 Dihedral : 4.256 21.779 1320 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1208 helix: 1.38 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -2.74 (0.42), residues: 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 218 time to evaluate : 1.127 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: 7 outliers final: 5 residues processed: 222 average time/residue: 0.2117 time to fit residues: 66.0448 Evaluate side-chains 208 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 203 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0975 time to fit residues: 2.4173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 9340 Z= 0.291 Angle : 0.872 17.810 12657 Z= 0.436 Chirality : 0.046 0.247 1502 Planarity : 0.005 0.068 1642 Dihedral : 4.620 24.889 1320 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 1.71 % 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: 0.72 (0.24), residues: 1208 helix: 1.05 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -2.62 (0.44), residues: 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 216 time to evaluate : 1.121 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 outliers start: 16 outliers final: 11 residues processed: 223 average time/residue: 0.2082 time to fit residues: 64.8304 Evaluate side-chains 212 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1274 time to fit residues: 3.5157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.0010 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 70 optimal weight: 0.0370 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 126 ASN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 9340 Z= 0.210 Angle : 0.889 19.529 12657 Z= 0.429 Chirality : 0.047 0.260 1502 Planarity : 0.004 0.050 1642 Dihedral : 4.473 22.973 1320 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.43 % 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: 0.99 (0.25), residues: 1208 helix: 1.23 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.55 (0.44), residues: 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 1.176 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: 4 outliers final: 3 residues processed: 214 average time/residue: 0.2135 time to fit residues: 63.7183 Evaluate side-chains 206 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1020 time to fit residues: 2.0661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 118 optimal weight: 0.0970 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 9340 Z= 0.254 Angle : 0.913 18.109 12657 Z= 0.449 Chirality : 0.049 0.271 1502 Planarity : 0.004 0.033 1642 Dihedral : 4.584 24.343 1320 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1208 helix: 1.06 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -2.61 (0.43), residues: 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 198 time to evaluate : 1.152 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: 6 outliers final: 4 residues processed: 201 average time/residue: 0.2519 time to fit residues: 71.9302 Evaluate side-chains 199 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 195 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0901 time to fit residues: 2.1357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 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 = 0.3828 r_free = 0.3828 target = 0.078565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.064721 restraints weight = 46628.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.065956 restraints weight = 34626.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.066844 restraints weight = 27131.641| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 9340 Z= 0.210 Angle : 0.902 18.975 12657 Z= 0.438 Chirality : 0.048 0.269 1502 Planarity : 0.004 0.034 1642 Dihedral : 4.482 23.280 1320 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.21 % 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: 0.85 (0.24), residues: 1208 helix: 1.12 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.49 (0.43), residues: 180 =============================================================================== Job complete usr+sys time: 1995.57 seconds wall clock time: 36 minutes 59.62 seconds (2219.62 seconds total)