Starting phenix.real_space_refine on Thu Dec 7 22:56:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/12_2023/7ul3_26590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/12_2023/7ul3_26590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/12_2023/7ul3_26590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/12_2023/7ul3_26590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/12_2023/7ul3_26590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/12_2023/7ul3_26590_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 31 5.16 5 C 3570 2.51 5 N 910 2.21 5 O 973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5484 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1944 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 7, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "C" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 807 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "H" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1300 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 9 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "L" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1413 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} Chain breaks: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FO9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.68, per 1000 atoms: 0.67 Number of scatterers: 5484 At special positions: 0 Unit cell: (65.9452, 80.6961, 157.921, 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 31 16.00 O 973 8.00 N 910 7.00 C 3570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 12 sheets defined 31.6% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 17 through 45 Processing helix chain 'A' and resid 52 through 69 removed outlier: 4.504A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.632A pdb=" N ILE A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 126 through 129 No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 132 through 154 Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.590A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 211 removed outlier: 3.541A pdb=" N LEU A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 260 Proline residue: A 249 - end of helix removed outlier: 3.527A pdb=" N GLY A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 291 removed outlier: 3.746A pdb=" N VAL A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 99 through 100B No H-bonds generated for 'chain 'H' and resid 99 through 100B' Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id= A, first strand: chain 'C' and resid 5 through 9 removed outlier: 3.596A pdb=" N GLN C 5 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 27 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 23 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 81 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 72 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 59 through 61 removed outlier: 6.893A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER C 52 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET C 36 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N THR C 54 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR C 34 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU C 100 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET C 36 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN C 98 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP C 38 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 96 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG C 40 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL C 94 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 98 through 102 Processing sheet with id= D, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.699A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.663A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.509A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 151 through 153 Processing sheet with id= H, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.248A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 21 through 24 removed outlier: 4.046A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 85 through 89 removed outlier: 5.900A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.790A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.824A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 741 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: 1.43 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 860 1.29 - 1.42: 1508 1.42 - 1.56: 3189 1.56 - 1.69: 3 1.69 - 1.83: 38 Bond restraints: 5598 Sorted by residual: bond pdb=" C5 FO9 A 401 " pdb=" S1 FO9 A 401 " ideal model delta sigma weight residual 1.802 1.541 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C6 FO9 A 401 " pdb=" S1 FO9 A 401 " ideal model delta sigma weight residual 1.771 1.550 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C4 FO9 A 401 " pdb=" N4 FO9 A 401 " ideal model delta sigma weight residual 1.284 1.452 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C4 FO9 A 401 " pdb=" C5 FO9 A 401 " ideal model delta sigma weight residual 1.516 1.377 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C THR L 74 " pdb=" O THR L 74 " ideal model delta sigma weight residual 1.234 1.154 0.080 1.22e-02 6.72e+03 4.30e+01 ... (remaining 5593 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.00: 115 106.00 - 113.00: 3046 113.00 - 120.00: 1836 120.00 - 126.99: 2600 126.99 - 133.99: 72 Bond angle restraints: 7669 Sorted by residual: angle pdb=" CA LEU L 73 " pdb=" C LEU L 73 " pdb=" N THR L 74 " ideal model delta sigma weight residual 115.51 123.82 -8.31 1.24e+00 6.50e-01 4.49e+01 angle pdb=" C THR L 22 " pdb=" CA THR L 22 " pdb=" CB THR L 22 " ideal model delta sigma weight residual 109.65 99.01 10.64 1.75e+00 3.27e-01 3.70e+01 angle pdb=" C2 FO9 A 401 " pdb=" S FO9 A 401 " pdb=" C3 FO9 A 401 " ideal model delta sigma weight residual 97.71 115.60 -17.89 3.00e+00 1.11e-01 3.56e+01 angle pdb=" CA THR L 74 " pdb=" C THR L 74 " pdb=" O THR L 74 " ideal model delta sigma weight residual 120.99 114.46 6.53 1.12e+00 7.97e-01 3.40e+01 angle pdb=" O FO9 A 401 " pdb=" S2 FO9 A 401 " pdb=" O1 FO9 A 401 " ideal model delta sigma weight residual 116.54 99.19 17.35 3.00e+00 1.11e-01 3.35e+01 ... (remaining 7664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3020 17.79 - 35.58: 161 35.58 - 53.37: 27 53.37 - 71.15: 7 71.15 - 88.94: 1 Dihedral angle restraints: 3216 sinusoidal: 997 harmonic: 2219 Sorted by residual: dihedral pdb=" CB CYS A 91 " pdb=" SG CYS A 91 " pdb=" SG CYS A 174 " pdb=" CB CYS A 174 " ideal model delta sinusoidal sigma weight residual -86.00 -156.31 70.31 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" C THR L 22 " pdb=" N THR L 22 " pdb=" CA THR L 22 " pdb=" CB THR L 22 " ideal model delta harmonic sigma weight residual -122.00 -108.53 -13.47 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" C THR L 20 " pdb=" N THR L 20 " pdb=" CA THR L 20 " pdb=" CB THR L 20 " ideal model delta harmonic sigma weight residual -122.00 -111.45 -10.55 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 3213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 700 0.047 - 0.093: 174 0.093 - 0.140: 47 0.140 - 0.187: 2 0.187 - 0.233: 5 Chirality restraints: 928 Sorted by residual: chirality pdb=" CA THR L 22 " pdb=" N THR L 22 " pdb=" C THR L 22 " pdb=" CB THR L 22 " both_signs ideal model delta sigma weight residual False 2.53 2.76 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA LEU L 73 " pdb=" N LEU L 73 " pdb=" C LEU L 73 " pdb=" CB LEU L 73 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA THR L 74 " pdb=" N THR L 74 " pdb=" C THR L 74 " pdb=" CB THR L 74 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 925 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 284 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 285 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR L 72 " 0.023 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C THR L 72 " -0.076 2.00e-02 2.50e+03 pdb=" O THR L 72 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU L 73 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 FO9 A 401 " -0.038 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" C6 FO9 A 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 FO9 A 401 " -0.002 2.00e-02 2.50e+03 pdb=" N1 FO9 A 401 " 0.019 2.00e-02 2.50e+03 pdb=" N2 FO9 A 401 " -0.050 2.00e-02 2.50e+03 pdb=" N3 FO9 A 401 " 0.039 2.00e-02 2.50e+03 pdb=" N4 FO9 A 401 " -0.015 2.00e-02 2.50e+03 pdb=" S1 FO9 A 401 " 0.019 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 506 2.75 - 3.29: 5135 3.29 - 3.82: 8560 3.82 - 4.36: 9676 4.36 - 4.90: 17581 Nonbonded interactions: 41458 Sorted by model distance: nonbonded pdb=" N PHE C 31 " pdb=" O ARG C 102 " model vdw 2.211 2.520 nonbonded pdb=" O ARG A 213 " pdb=" NH2 ARG C 102 " model vdw 2.324 2.520 nonbonded pdb=" OD1 ASP H 101 " pdb=" N TYR H 102 " model vdw 2.355 2.520 nonbonded pdb=" O ASN A 280 " pdb=" OD1 ASN A 280 " model vdw 2.364 3.040 nonbonded pdb=" NH1 ARG A 230 " pdb=" O ILE C 105 " model vdw 2.388 2.520 ... (remaining 41453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.000 Extract box with map and model: 11.310 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.500 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.261 5598 Z= 0.520 Angle : 0.876 17.894 7669 Z= 0.482 Chirality : 0.046 0.233 928 Planarity : 0.007 0.114 952 Dihedral : 11.481 88.942 1768 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.57 % 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: 1.41 (0.30), residues: 727 helix: 2.31 (0.32), residues: 228 sheet: 1.24 (0.36), residues: 198 loop : -0.34 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 100G HIS 0.010 0.002 HIS H 200 PHE 0.019 0.002 PHE A 191 TYR 0.028 0.002 TYR C 81 ARG 0.005 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.628 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.6806 time to fit residues: 47.3373 Evaluate side-chains 41 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 67 optimal weight: 20.0000 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN H 200 HIS L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5598 Z= 0.158 Angle : 0.532 6.324 7669 Z= 0.279 Chirality : 0.041 0.136 928 Planarity : 0.005 0.068 952 Dihedral : 4.984 59.290 821 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.25 % Allowed : 8.18 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.83 (0.31), residues: 727 helix: 2.64 (0.32), residues: 233 sheet: 1.72 (0.35), residues: 206 loop : -0.41 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 275 HIS 0.002 0.001 HIS L 189 PHE 0.012 0.001 PHE H 27 TYR 0.016 0.002 TYR A 78 ARG 0.007 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.609 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 43 average time/residue: 0.7789 time to fit residues: 36.4388 Evaluate side-chains 37 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.2056 time to fit residues: 1.1222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 66 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 54 optimal weight: 20.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5598 Z= 0.314 Angle : 0.608 6.282 7669 Z= 0.324 Chirality : 0.044 0.145 928 Planarity : 0.005 0.059 952 Dihedral : 5.307 55.608 821 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.68 % Allowed : 10.43 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.31), residues: 727 helix: 1.84 (0.33), residues: 240 sheet: 1.57 (0.37), residues: 197 loop : -0.63 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.002 PHE H 27 TYR 0.020 0.002 TYR A 94 ARG 0.003 0.000 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 0.585 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 51 average time/residue: 0.7327 time to fit residues: 40.5582 Evaluate side-chains 44 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 1 average time/residue: 0.2070 time to fit residues: 1.0488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN H 39 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 5598 Z= 0.431 Angle : 0.653 6.259 7669 Z= 0.353 Chirality : 0.046 0.159 928 Planarity : 0.005 0.051 952 Dihedral : 5.445 49.775 821 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.50 % Allowed : 11.45 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.31), residues: 727 helix: 1.25 (0.33), residues: 240 sheet: 1.06 (0.36), residues: 211 loop : -0.96 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.022 0.002 PHE H 27 TYR 0.023 0.003 TYR L 49 ARG 0.002 0.001 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 41 time to evaluate : 0.588 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 55 average time/residue: 0.5914 time to fit residues: 35.8068 Evaluate side-chains 54 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.1189 time to fit residues: 1.2745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5598 Z= 0.231 Angle : 0.534 5.566 7669 Z= 0.281 Chirality : 0.041 0.136 928 Planarity : 0.004 0.044 952 Dihedral : 4.857 42.718 821 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.29 % Allowed : 12.47 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.83 (0.31), residues: 727 helix: 1.64 (0.34), residues: 239 sheet: 1.13 (0.36), residues: 214 loop : -0.90 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.001 PHE H 27 TYR 0.014 0.002 TYR A 94 ARG 0.002 0.000 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.656 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 56 average time/residue: 0.5968 time to fit residues: 36.9443 Evaluate side-chains 56 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 5 average time/residue: 0.3124 time to fit residues: 2.5557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5598 Z= 0.180 Angle : 0.500 6.918 7669 Z= 0.261 Chirality : 0.040 0.131 928 Planarity : 0.004 0.039 952 Dihedral : 4.481 38.842 821 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.48 % Allowed : 14.93 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.01 (0.31), residues: 727 helix: 1.84 (0.34), residues: 239 sheet: 1.18 (0.36), residues: 214 loop : -0.81 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.002 0.001 HIS L 189 PHE 0.012 0.001 PHE H 27 TYR 0.017 0.001 TYR A 78 ARG 0.002 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.630 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 54 average time/residue: 0.5767 time to fit residues: 34.5861 Evaluate side-chains 53 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.1083 time to fit residues: 1.4148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5598 Z= 0.269 Angle : 0.545 5.628 7669 Z= 0.290 Chirality : 0.041 0.141 928 Planarity : 0.004 0.038 952 Dihedral : 4.687 38.631 821 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.27 % Allowed : 15.75 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.84 (0.31), residues: 727 helix: 1.77 (0.34), residues: 238 sheet: 1.07 (0.37), residues: 215 loop : -0.97 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.002 0.001 HIS L 189 PHE 0.015 0.002 PHE H 27 TYR 0.023 0.002 TYR A 94 ARG 0.002 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.639 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 52 average time/residue: 0.6178 time to fit residues: 35.4916 Evaluate side-chains 52 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.1099 time to fit residues: 1.3699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 5598 Z= 0.420 Angle : 0.635 6.415 7669 Z= 0.343 Chirality : 0.045 0.154 928 Planarity : 0.005 0.039 952 Dihedral : 5.230 48.135 821 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.68 % Allowed : 15.95 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.34 (0.30), residues: 727 helix: 1.40 (0.33), residues: 235 sheet: 0.85 (0.36), residues: 216 loop : -1.34 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.002 PHE C 39 TYR 0.026 0.002 TYR A 94 ARG 0.003 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.584 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 62 average time/residue: 0.5684 time to fit residues: 38.8895 Evaluate side-chains 62 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.1020 time to fit residues: 1.3924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 40.0000 chunk 68 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5598 Z= 0.319 Angle : 0.599 7.912 7669 Z= 0.313 Chirality : 0.043 0.144 928 Planarity : 0.004 0.038 952 Dihedral : 5.029 46.975 821 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.89 % Allowed : 16.77 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.37 (0.31), residues: 727 helix: 1.43 (0.34), residues: 238 sheet: 0.79 (0.36), residues: 214 loop : -1.28 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.002 PHE C 39 TYR 0.024 0.002 TYR A 94 ARG 0.003 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 0.714 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 56 average time/residue: 0.5242 time to fit residues: 32.7956 Evaluate side-chains 52 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 2 average time/residue: 0.1264 time to fit residues: 1.1008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 73 optimal weight: 50.0000 chunk 67 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.0270 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5598 Z= 0.196 Angle : 0.528 9.428 7669 Z= 0.271 Chirality : 0.040 0.131 928 Planarity : 0.004 0.037 952 Dihedral : 4.638 42.785 821 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.25 % Allowed : 18.20 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.66 (0.31), residues: 727 helix: 1.76 (0.34), residues: 238 sheet: 0.88 (0.36), residues: 213 loop : -1.12 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE C 39 TYR 0.019 0.002 TYR A 94 ARG 0.002 0.000 ARG H 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.612 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 51 average time/residue: 0.5664 time to fit residues: 32.1085 Evaluate side-chains 49 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 0.8332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.242682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.166414 restraints weight = 7058.894| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 3.67 r_work: 0.3881 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5598 Z= 0.191 Angle : 0.524 8.876 7669 Z= 0.268 Chirality : 0.040 0.131 928 Planarity : 0.004 0.036 952 Dihedral : 4.488 41.169 821 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.66 % Allowed : 17.59 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.87 (0.32), residues: 727 helix: 1.92 (0.34), residues: 237 sheet: 0.92 (0.36), residues: 221 loop : -0.97 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 275 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE C 39 TYR 0.019 0.001 TYR A 94 ARG 0.002 0.000 ARG H 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.67 seconds wall clock time: 33 minutes 4.07 seconds (1984.07 seconds total)