Starting phenix.real_space_refine (version: dev) on Sat Feb 18 19:56:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2v_32972/02_2023/7x2v_32972_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2v_32972/02_2023/7x2v_32972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2v_32972/02_2023/7x2v_32972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2v_32972/02_2023/7x2v_32972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2v_32972/02_2023/7x2v_32972_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2v_32972/02_2023/7x2v_32972_neut.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 Process input model Symmetric amino acids flipped Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8755 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1769 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2179 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Time building chain proxies: 5.08, per 1000 atoms: 0.58 Number of scatterers: 8755 At special positions: 0 Unit cell: (88, 121, 130.9, 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 61 16.00 O 1616 8.00 N 1479 7.00 C 5599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.03 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: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.714A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.999A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 241 through 255 removed outlier: 4.142A pdb=" N GLU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.841A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.512A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 removed outlier: 4.047A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.559A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 568 through 572 removed outlier: 3.528A pdb=" N ILE R 571 " --> pdb=" O SER R 568 " (cutoff:3.500A) Processing helix chain 'R' and resid 578 through 580 No H-bonds generated for 'chain 'R' and resid 578 through 580' Processing helix chain 'R' and resid 581 through 610 removed outlier: 3.667A pdb=" N LYS R 586 " --> pdb=" O PHE R 582 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY R 598 " --> pdb=" O GLY R 594 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU R 602 " --> pdb=" O GLY R 598 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE R 610 " --> pdb=" O ILE R 606 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 614 removed outlier: 3.805A pdb=" N ILE R 614 " --> pdb=" O TRP R 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 611 through 614' Processing helix chain 'R' and resid 617 through 647 removed outlier: 3.719A pdb=" N HIS R 621 " --> pdb=" O SER R 617 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 688 removed outlier: 3.736A pdb=" N PHE R 672 " --> pdb=" O TYR R 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 694 through 707 Processing helix chain 'R' and resid 709 through 722 removed outlier: 3.550A pdb=" N SER R 714 " --> pdb=" O PRO R 710 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL R 715 " --> pdb=" O LEU R 711 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE R 718 " --> pdb=" O SER R 714 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA R 719 " --> pdb=" O VAL R 715 " (cutoff:3.500A) Processing helix chain 'R' and resid 723 through 725 No H-bonds generated for 'chain 'R' and resid 723 through 725' Processing helix chain 'R' and resid 743 through 746 Processing helix chain 'R' and resid 747 through 754 removed outlier: 3.773A pdb=" N ILE R 754 " --> pdb=" O PRO R 750 " (cutoff:3.500A) Processing helix chain 'R' and resid 754 through 770 removed outlier: 3.902A pdb=" N LYS R 768 " --> pdb=" O LEU R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 797 Processing helix chain 'R' and resid 802 through 810 Processing helix chain 'R' and resid 818 through 828 removed outlier: 3.871A pdb=" N ILE R 822 " --> pdb=" O ALA R 818 " (cutoff:3.500A) Processing helix chain 'R' and resid 829 through 838 Processing helix chain 'R' and resid 842 through 853 Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.723A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.634A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.638A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.612A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 182 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.155A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.415A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.503A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.540A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.710A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.672A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.106A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2789 1.34 - 1.47: 2241 1.47 - 1.59: 3820 1.59 - 1.72: 0 1.72 - 1.84: 89 Bond restraints: 8939 Sorted by residual: bond pdb=" N VAL R 812 " pdb=" CA VAL R 812 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.70e+00 bond pdb=" N ILE R 811 " pdb=" CA ILE R 811 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.41e-02 5.03e+03 7.54e+00 bond pdb=" N ASP R 813 " pdb=" CA ASP R 813 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.92e+00 bond pdb=" N ASN R 816 " pdb=" CA ASN R 816 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.74e+00 bond pdb=" N LEU R 817 " pdb=" CA LEU R 817 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.67e+00 ... (remaining 8934 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.86: 148 105.86 - 112.92: 4833 112.92 - 119.98: 3093 119.98 - 127.05: 3928 127.05 - 134.11: 109 Bond angle restraints: 12111 Sorted by residual: angle pdb=" N ASP B 309 " pdb=" CA ASP B 309 " pdb=" C ASP B 309 " ideal model delta sigma weight residual 111.71 117.95 -6.24 1.15e+00 7.56e-01 2.95e+01 angle pdb=" C LEU B 268 " pdb=" CA LEU B 268 " pdb=" CB LEU B 268 " ideal model delta sigma weight residual 109.48 117.16 -7.68 1.68e+00 3.54e-01 2.09e+01 angle pdb=" N LEU B 268 " pdb=" CA LEU B 268 " pdb=" C LEU B 268 " ideal model delta sigma weight residual 109.76 102.68 7.08 1.64e+00 3.72e-01 1.86e+01 angle pdb=" C VAL E 48 " pdb=" N ALA E 49 " pdb=" CA ALA E 49 " ideal model delta sigma weight residual 121.75 115.08 6.67 1.73e+00 3.34e-01 1.48e+01 angle pdb=" N ASP C 205 " pdb=" CA ASP C 205 " pdb=" C ASP C 205 " ideal model delta sigma weight residual 111.71 106.60 5.11 1.34e+00 5.57e-01 1.46e+01 ... (remaining 12106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 4898 16.66 - 33.31: 315 33.31 - 49.97: 52 49.97 - 66.62: 13 66.62 - 83.28: 3 Dihedral angle restraints: 5281 sinusoidal: 2044 harmonic: 3237 Sorted by residual: dihedral pdb=" CA ASP C 163 " pdb=" C ASP C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA C 305 " pdb=" C ALA C 305 " pdb=" N GLY C 306 " pdb=" CA GLY C 306 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP B 309 " pdb=" C ASP B 309 " pdb=" N LEU B 310 " pdb=" CA LEU B 310 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1154 0.070 - 0.140: 214 0.140 - 0.210: 18 0.210 - 0.280: 5 0.280 - 0.350: 1 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CG LEU E 162 " pdb=" CB LEU E 162 " pdb=" CD1 LEU E 162 " pdb=" CD2 LEU E 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA LEU B 283 " pdb=" N LEU B 283 " pdb=" C LEU B 283 " pdb=" CB LEU B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASP C 291 " pdb=" N ASP C 291 " pdb=" C ASP C 291 " pdb=" CB ASP C 291 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1389 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 169 " -0.031 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP C 169 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 169 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 169 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 169 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 169 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 169 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 54 " 0.042 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO D 55 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 339 " 0.021 2.00e-02 2.50e+03 1.56e-02 6.05e+00 pdb=" CG TRP C 339 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 339 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C 339 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 339 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 339 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 339 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 339 " 0.000 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 182 2.67 - 3.23: 8382 3.23 - 3.79: 13474 3.79 - 4.34: 17564 4.34 - 4.90: 29538 Nonbonded interactions: 69140 Sorted by model distance: nonbonded pdb=" O ARG C 219 " pdb=" NE2 GLN C 220 " model vdw 2.115 2.520 nonbonded pdb=" ND2 ASN R 758 " pdb=" O LEU R 800 " model vdw 2.173 2.520 nonbonded pdb=" O CYS C 103 " pdb=" NH2 ARG C 150 " model vdw 2.181 2.520 nonbonded pdb=" N GLY C 144 " pdb=" OD2 ASP C 163 " model vdw 2.209 2.520 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.239 2.440 ... (remaining 69135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5599 2.51 5 N 1479 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.190 Check model and map are aligned: 0.140 Process input model: 24.840 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 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 0.068 8939 Z= 0.460 Angle : 0.927 10.260 12111 Z= 0.542 Chirality : 0.054 0.350 1392 Planarity : 0.005 0.065 1516 Dihedral : 11.889 83.276 3185 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.89 (0.24), residues: 1104 helix: 0.76 (0.29), residues: 338 sheet: -0.19 (0.29), residues: 294 loop : -1.86 (0.26), residues: 472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.933 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.2215 time to fit residues: 40.1243 Evaluate side-chains 116 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0970 time to fit residues: 1.6512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.0570 chunk 99 optimal weight: 0.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8939 Z= 0.194 Angle : 0.624 7.885 12111 Z= 0.333 Chirality : 0.044 0.162 1392 Planarity : 0.004 0.052 1516 Dihedral : 5.173 22.150 1199 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.33 (0.25), residues: 1104 helix: 1.62 (0.29), residues: 342 sheet: -0.08 (0.29), residues: 279 loop : -1.70 (0.26), residues: 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.981 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.2268 time to fit residues: 38.2762 Evaluate side-chains 129 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0873 time to fit residues: 3.3940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 68 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.0370 chunk 80 optimal weight: 0.0060 overall best weight: 0.1274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8939 Z= 0.146 Angle : 0.548 7.660 12111 Z= 0.290 Chirality : 0.042 0.148 1392 Planarity : 0.004 0.051 1516 Dihedral : 4.612 21.627 1199 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.10 (0.25), residues: 1104 helix: 2.12 (0.29), residues: 344 sheet: 0.00 (0.30), residues: 283 loop : -1.49 (0.26), residues: 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.980 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 132 average time/residue: 0.2257 time to fit residues: 41.0171 Evaluate side-chains 117 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0988 time to fit residues: 2.0883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 8939 Z= 0.301 Angle : 0.665 9.760 12111 Z= 0.350 Chirality : 0.045 0.152 1392 Planarity : 0.004 0.046 1516 Dihedral : 4.979 26.925 1199 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.04 (0.25), residues: 1104 helix: 2.09 (0.29), residues: 343 sheet: 0.08 (0.30), residues: 292 loop : -1.64 (0.27), residues: 469 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.891 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.2252 time to fit residues: 39.4425 Evaluate side-chains 132 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0850 time to fit residues: 3.2165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 40.0000 chunk 79 optimal weight: 50.0000 chunk 43 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 chunk 0 optimal weight: 50.0000 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8939 Z= 0.171 Angle : 0.583 9.903 12111 Z= 0.304 Chirality : 0.042 0.150 1392 Planarity : 0.004 0.049 1516 Dihedral : 4.616 27.203 1199 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.19 (0.26), residues: 1104 helix: 2.35 (0.29), residues: 345 sheet: 0.02 (0.30), residues: 293 loop : -1.57 (0.27), residues: 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.964 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 127 average time/residue: 0.2057 time to fit residues: 36.5257 Evaluate side-chains 121 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0861 time to fit residues: 2.3276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.0050 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8939 Z= 0.189 Angle : 0.581 10.155 12111 Z= 0.304 Chirality : 0.042 0.183 1392 Planarity : 0.004 0.049 1516 Dihedral : 4.548 27.453 1199 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.29 (0.26), residues: 1104 helix: 2.53 (0.29), residues: 344 sheet: -0.01 (0.29), residues: 297 loop : -1.53 (0.27), residues: 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.971 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 123 average time/residue: 0.2196 time to fit residues: 37.7238 Evaluate side-chains 115 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0838 time to fit residues: 2.3449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.0570 chunk 42 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8939 Z= 0.199 Angle : 0.596 9.158 12111 Z= 0.311 Chirality : 0.043 0.149 1392 Planarity : 0.004 0.055 1516 Dihedral : 4.543 28.127 1199 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.18 (0.26), residues: 1104 helix: 2.27 (0.29), residues: 353 sheet: -0.01 (0.30), residues: 297 loop : -1.58 (0.27), residues: 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.988 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 120 average time/residue: 0.2330 time to fit residues: 38.8032 Evaluate side-chains 124 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0923 time to fit residues: 2.7237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.0470 chunk 83 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 691 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 8939 Z= 0.159 Angle : 0.573 10.728 12111 Z= 0.295 Chirality : 0.043 0.148 1392 Planarity : 0.004 0.056 1516 Dihedral : 4.412 27.734 1199 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.22 (0.26), residues: 1104 helix: 2.31 (0.29), residues: 352 sheet: -0.03 (0.29), residues: 297 loop : -1.52 (0.28), residues: 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.997 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 126 average time/residue: 0.2313 time to fit residues: 40.5559 Evaluate side-chains 122 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0839 time to fit residues: 2.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 77 optimal weight: 40.0000 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 0.0030 chunk 93 optimal weight: 0.0980 chunk 64 optimal weight: 0.0000 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8939 Z= 0.148 Angle : 0.574 12.066 12111 Z= 0.291 Chirality : 0.042 0.154 1392 Planarity : 0.004 0.059 1516 Dihedral : 4.241 26.916 1199 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.33 (0.26), residues: 1104 helix: 2.46 (0.29), residues: 352 sheet: -0.06 (0.30), residues: 294 loop : -1.43 (0.27), residues: 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.039 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 119 average time/residue: 0.2339 time to fit residues: 38.5775 Evaluate side-chains 117 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0970 time to fit residues: 1.8232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.0270 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5802 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8939 Z= 0.176 Angle : 0.604 13.983 12111 Z= 0.304 Chirality : 0.043 0.221 1392 Planarity : 0.004 0.059 1516 Dihedral : 4.288 27.226 1199 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1104 helix: 2.42 (0.29), residues: 354 sheet: 0.01 (0.30), residues: 298 loop : -1.46 (0.27), residues: 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.952 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 117 average time/residue: 0.2274 time to fit residues: 36.9367 Evaluate side-chains 118 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0821 time to fit residues: 1.8479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.203141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.175331 restraints weight = 12491.940| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.90 r_work: 0.4289 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8939 Z= 0.177 Angle : 0.609 13.121 12111 Z= 0.305 Chirality : 0.043 0.187 1392 Planarity : 0.004 0.056 1516 Dihedral : 4.310 27.525 1199 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.36 (0.26), residues: 1104 helix: 2.43 (0.29), residues: 354 sheet: 0.08 (0.30), residues: 297 loop : -1.49 (0.27), residues: 453 =============================================================================== Job complete usr+sys time: 2138.47 seconds wall clock time: 39 minutes 56.52 seconds (2396.52 seconds total)