Starting phenix.real_space_refine on Sun May 19 16:32:01 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.65 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8fsj_29419.map" } resolution = 3.65 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } 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= 0.011 sd= 0.089 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 6044 2.51 5 N 1646 2.21 5 O 1884 1.98 5 H 9288 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 18915 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4331 Classifications: {'peptide': 284} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 260} Chain: "H" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3307 Inner-chain residues flagged as termini: ['pdbres="SER H 127 "', 'pdbres="SER H 132 "'] Classifications: {'peptide': 225} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3244 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1225 Inner-chain residues flagged as termini: ['pdbres="THR A 255 "', 'pdbres="PRO A 295 "'] Classifications: {'peptide': 82} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain breaks: 1 Chain: "B" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3191 Inner-chain residues flagged as termini: ['pdbres="GLY B 128 "'] Classifications: {'peptide': 211} Modifications used: {'COO': 1, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain: "C" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3617 Classifications: {'peptide': 242} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Time building chain proxies: 5.43, per 1000 atoms: 0.29 Number of scatterers: 18915 At special positions: 0 Unit cell: (72.009, 139.573, 139.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 O 1884 8.00 N 1646 7.00 C 6044 6.00 H 9288 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 429 " - pdb=" SG CYS E 503 " distance=2.03 Simple disulfide: pdb=" SG CYS E 452 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS E 486 " distance=2.04 Simple disulfide: pdb=" SG CYS E 494 " - pdb=" SG CYS E 564 " distance=2.04 Simple disulfide: pdb=" SG CYS E 508 " - pdb=" SG CYS E 552 " distance=2.03 Simple disulfide: pdb=" SG CYS E 569 " - pdb=" SG CYS E 597 " distance=2.03 Simple disulfide: pdb=" SG CYS E 581 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 607 " - pdb=" SG CYS E 644 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 677 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 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 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 304 " distance=2.04 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.05 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: 7.92 Conformation dependent library (CDL) restraints added in 1.2 seconds Finding SS restraints... Secondary structure from input PDB file: 20 helices and 26 sheets defined 6.8% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'E' and resid 437 through 442 Processing helix chain 'E' and resid 449 through 455 Proline residue: E 453 - end of helix Processing helix chain 'E' and resid 594 through 597 No H-bonds generated for 'chain 'E' and resid 594 through 597' Processing helix chain 'E' and resid 614 through 617 No H-bonds generated for 'chain 'E' and resid 614 through 617' 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 154 through 157 Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 122 through 126 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 186 through 191 removed outlier: 3.632A pdb=" N GLY C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing sheet with id= A, first strand: chain 'E' and resid 507 through 509 removed outlier: 3.950A pdb=" N GLY E 551 " --> pdb=" O PHE E 509 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 671 through 673 removed outlier: 3.551A pdb=" N GLN E 700 " --> pdb=" O TRP E 672 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= D, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.036A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN H 39 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE H 34 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.715A pdb=" N LYS H 143 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 150 through 154 removed outlier: 3.712A pdb=" N SER H 153 " --> pdb=" O ASN H 197 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 93 through 97 removed outlier: 4.613A pdb=" N ARG H 94 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU H 96 " --> pdb=" O VAL H 100J" (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL H 100J" --> pdb=" O LEU H 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.773A pdb=" N VAL H 142 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.717A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.095A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.579A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 116 through 118 Processing sheet with id= M, first strand: chain 'L' and resid 153 through 155 removed outlier: 3.735A pdb=" N GLN L 155 " --> pdb=" O TRP L 148 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.672A pdb=" N HIS A 202 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 229 through 232 removed outlier: 4.307A pdb=" N VAL A 230 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG A 237 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.891A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.537A pdb=" N ARG B 103 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU B 13 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU B 105 " --> pdb=" O LEU B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'B' and resid 19 through 21 Processing sheet with id= S, first strand: chain 'B' and resid 85 through 88 removed outlier: 3.785A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.546A pdb=" N SER B 114 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 137 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR B 172 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 144 through 149 removed outlier: 3.540A pdb=" N VAL B 204 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 10 through 12 Processing sheet with id= W, first strand: chain 'C' and resid 70 through 72 removed outlier: 3.521A pdb=" N SER C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.829A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.509A pdb=" N THR C 151 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 35 through 38 removed outlier: 5.709A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 519 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: 6.47 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.15: 9288 1.15 - 1.33: 1699 1.33 - 1.50: 4305 1.50 - 1.68: 3808 1.68 - 1.86: 64 Bond restraints: 19164 Sorted by residual: bond pdb=" NH1 ARG B 141 " pdb="HH12 ARG B 141 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" NH2 ARG C 19 " pdb="HH21 ARG C 19 " ideal model delta sigma weight residual 0.860 1.033 -0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" CE1 TYR L 49 " pdb=" HE1 TYR L 49 " ideal model delta sigma weight residual 0.930 1.102 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" CE2 TYR H 99 " pdb=" HE2 TYR H 99 " ideal model delta sigma weight residual 0.930 1.102 -0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" NH1 ARG B 141 " pdb="HH11 ARG B 141 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.13e+01 ... (remaining 19159 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.16: 256 105.16 - 112.38: 21756 112.38 - 119.60: 4758 119.60 - 126.82: 7576 126.82 - 134.03: 190 Bond angle restraints: 34536 Sorted by residual: angle pdb=" N ALA H 88 " pdb=" CA ALA H 88 " pdb=" C ALA H 88 " ideal model delta sigma weight residual 107.73 114.31 -6.58 1.61e+00 3.86e-01 1.67e+01 angle pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " pdb=" CG TYR H 99 " ideal model delta sigma weight residual 113.90 107.19 6.71 1.80e+00 3.09e-01 1.39e+01 angle pdb=" C ARG E 587 " pdb=" N LYS E 588 " pdb=" CA LYS E 588 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.28e+00 angle pdb=" C SER C 179 " pdb=" N SER C 180 " pdb=" CA SER C 180 " ideal model delta sigma weight residual 121.75 116.83 4.92 1.73e+00 3.34e-01 8.09e+00 angle pdb=" N ARG B 141 " pdb=" CA ARG B 141 " pdb=" C ARG B 141 " ideal model delta sigma weight residual 110.35 114.11 -3.76 1.38e+00 5.25e-01 7.42e+00 ... (remaining 34531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 6072 18.40 - 36.81: 617 36.81 - 55.21: 225 55.21 - 73.61: 30 73.61 - 92.02: 11 Dihedral angle restraints: 6955 sinusoidal: 4989 harmonic: 1966 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -138.44 52.44 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS E 569 " pdb=" SG CYS E 569 " pdb=" SG CYS E 597 " pdb=" CB CYS E 597 " ideal model delta sinusoidal sigma weight residual 93.00 143.64 -50.64 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS E 452 " pdb=" SG CYS E 452 " pdb=" SG CYS E 620 " pdb=" CB CYS E 620 " ideal model delta sinusoidal sigma weight residual -86.00 -130.46 44.46 1 1.00e+01 1.00e-02 2.75e+01 ... (remaining 6952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 933 0.034 - 0.068: 381 0.068 - 0.102: 104 0.102 - 0.136: 71 0.136 - 0.170: 10 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CA VAL C 181 " pdb=" N VAL C 181 " pdb=" C VAL C 181 " pdb=" CB VAL C 181 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ILE C 50 " pdb=" N ILE C 50 " pdb=" C ILE C 50 " pdb=" CB ILE C 50 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA VAL H 11 " pdb=" N VAL H 11 " pdb=" C VAL H 11 " pdb=" CB VAL H 11 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1496 not shown) Planarity restraints: 2906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 99 " -0.022 2.00e-02 2.50e+03 1.60e-02 7.65e+00 pdb=" CG TYR H 99 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 99 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR H 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR H 99 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 99 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR H 99 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR H 99 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 TYR H 99 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR H 99 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TYR H 99 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 TYR H 99 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.028 2.00e-02 2.50e+03 1.53e-02 6.98e+00 pdb=" CG TYR L 49 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR L 49 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR L 49 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR L 49 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR L 49 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 99 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C TYR H 99 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR H 99 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS H 100 " 0.014 2.00e-02 2.50e+03 ... (remaining 2903 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 918 2.08 - 2.71: 28246 2.71 - 3.34: 51221 3.34 - 3.97: 69059 3.97 - 4.60: 100874 Nonbonded interactions: 250318 Sorted by model distance: nonbonded pdb=" O ALA A 251 " pdb=" HG1 THR A 255 " model vdw 1.452 1.850 nonbonded pdb=" O ASN E 540 " pdb="HD21 ASN E 548 " model vdw 1.455 1.850 nonbonded pdb=" O SER B 127 " pdb=" H1 GLY B 128 " model vdw 1.479 1.960 nonbonded pdb=" O ASP E 658 " pdb=" HG SER E 678 " model vdw 1.490 1.850 nonbonded pdb=" OD1 ASP L 170 " pdb=" HG1 THR L 172 " model vdw 1.507 1.850 ... (remaining 250313 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined 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: 0.060 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 34.930 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:27.020 Internal consistency checks: 0.000 Total: 63.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.003 0.061 9876 Z= 0.215 Angle : 0.641 6.709 13471 Z= 0.341 Chirality : 0.045 0.170 1499 Planarity : 0.005 0.057 1739 Dihedral : 12.887 92.017 3532 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.65 % Allowed : 2.21 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.23), residues: 1241 helix: -3.01 (0.56), residues: 48 sheet: -0.60 (0.25), residues: 444 loop : -1.50 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 77 TYR 0.039 0.002 TYR H 99 PHE 0.009 0.001 PHE E 509 TRP 0.016 0.001 TRP C 154 HIS 0.006 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9876 Z= 0.348 Angle : 0.655 5.908 13471 Z= 0.347 Chirality : 0.064 0.243 1499 Planarity : 0.006 0.063 1739 Dihedral : 12.232 86.754 3532 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 2.18 % Allowed : 13.13 % Favored : 84.69 % Rotamer: Outliers : 1.20 % Allowed : 4.15 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.21), residues: 1241 helix: -3.49 (0.49), residues: 49 sheet: -1.92 (0.22), residues: 437 loop : -2.89 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 94 TYR 0.017 0.002 TYR B 91 PHE 0.018 0.002 PHE E 465 TRP 0.015 0.002 TRP C 47 HIS 0.008 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 61 optimal weight: 60.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 116 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 overall best weight: 11.1996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 9876 Z= 0.542 Angle : 0.740 8.384 13471 Z= 0.396 Chirality : 0.069 0.241 1499 Planarity : 0.006 0.074 1739 Dihedral : 12.864 86.407 3532 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 4.35 % Allowed : 17.65 % Favored : 78.00 % Rotamer: Outliers : 2.31 % Allowed : 7.20 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.19), residues: 1241 helix: -3.56 (0.50), residues: 49 sheet: -2.57 (0.22), residues: 413 loop : -3.94 (0.18), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 38 TYR 0.017 0.002 TYR L 49 PHE 0.024 0.002 PHE E 509 TRP 0.015 0.003 TRP C 154 HIS 0.012 0.002 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 90 optimal weight: 50.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9876 Z= 0.374 Angle : 0.614 7.728 13471 Z= 0.322 Chirality : 0.064 0.223 1499 Planarity : 0.005 0.058 1739 Dihedral : 12.453 84.369 3532 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 4.11 % Allowed : 15.63 % Favored : 80.26 % Rotamer: Outliers : 2.49 % Allowed : 7.75 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -5.14 (0.19), residues: 1241 helix: -3.86 (0.45), residues: 49 sheet: -2.77 (0.22), residues: 411 loop : -3.97 (0.17), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 543 TYR 0.013 0.002 TYR B 91 PHE 0.021 0.002 PHE E 509 TRP 0.012 0.002 TRP C 103 HIS 0.009 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 50.0000 chunk 115 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 chunk 9 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 80.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9876 Z= 0.404 Angle : 0.629 6.847 13471 Z= 0.331 Chirality : 0.065 0.234 1499 Planarity : 0.006 0.066 1739 Dihedral : 12.509 89.013 3532 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 5.08 % Allowed : 18.13 % Favored : 76.79 % Rotamer: Outliers : 3.32 % Allowed : 7.75 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -5.44 (0.19), residues: 1241 helix: -3.92 (0.48), residues: 49 sheet: -2.90 (0.21), residues: 419 loop : -4.24 (0.17), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 100G TYR 0.014 0.002 TYR B 91 PHE 0.021 0.002 PHE E 509 TRP 0.013 0.002 TRP C 154 HIS 0.010 0.001 HIS C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 116 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 9876 Z= 0.440 Angle : 0.670 7.111 13471 Z= 0.355 Chirality : 0.066 0.237 1499 Planarity : 0.006 0.061 1739 Dihedral : 12.942 87.516 3532 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 6.69 % Allowed : 18.29 % Favored : 75.02 % Rotamer: Outliers : 4.34 % Allowed : 9.13 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.18), residues: 1241 helix: -4.14 (0.43), residues: 48 sheet: -3.08 (0.22), residues: 410 loop : -4.48 (0.16), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 543 TYR 0.014 0.002 TYR B 91 PHE 0.023 0.002 PHE E 509 TRP 0.013 0.002 TRP C 103 HIS 0.009 0.001 HIS C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 394.97 seconds wall clock time: 7 minutes 44.44 seconds (464.44 seconds total)