Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 03:58:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/10_2023/7thm_25898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/10_2023/7thm_25898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/10_2023/7thm_25898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/10_2023/7thm_25898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/10_2023/7thm_25898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/10_2023/7thm_25898_updated.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.076 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: 8 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 P 2 5.49 5 S 66 5.16 5 C 5908 2.51 5 N 1543 2.21 5 O 1693 1.98 5 H 9045 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 18260 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 13640 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 30, 'TRANS': 829} Chain breaks: 11 Chain: "B" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1684 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 2 Chain: "C" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 586 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain breaks: 1 Chain: "D" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1139 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 4 Chain: "G" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1199 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain breaks: 4 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' MN': 1, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4485 SG CYS A 301 81.783 64.126 47.676 1.00 48.64 S ATOM 4562 SG CYS A 306 84.380 62.568 45.313 1.00 47.32 S ATOM 4626 SG CYS A 310 83.281 60.731 48.499 1.00 44.89 S ATOM 7312 SG CYS A 487 68.846 76.054 38.528 1.00 57.90 S ATOM 9765 SG CYS A 645 71.609 75.822 35.848 1.00 61.34 S ATOM 9775 SG CYS A 646 72.472 76.310 39.541 1.00 58.02 S Time building chain proxies: 8.20, per 1000 atoms: 0.45 Number of scatterers: 18260 At special positions: 0 Unit cell: (130.186, 99.554, 101.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 66 16.00 P 2 15.00 O 1693 8.00 N 1543 7.00 C 5908 6.00 H 9045 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.67 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 10 sheets defined 39.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.568A pdb=" N ILE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.618A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.659A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.193A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.691A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.840A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 482 removed outlier: 3.713A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N CYS A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 562 through 580 removed outlier: 4.377A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 639 Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 719 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 856 through 871 removed outlier: 3.594A pdb=" N TYR A 867 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 875 through 890 removed outlier: 4.108A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 4.011A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.585A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.655A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 35 through 40 removed outlier: 3.875A pdb=" N ILE C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.922A pdb=" N MET C 52 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 53 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 55 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 57 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 98 Processing helix chain 'D' and resid 101 through 110 removed outlier: 3.508A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.621A pdb=" N ARG A 33 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 72 through 74 Processing sheet with id= D, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.527A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 753 through 758 Processing sheet with id= F, first strand: chain 'A' and resid 816 through 820 Processing sheet with id= G, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.532A pdb=" N LEU B 128 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.956A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 147 through 149 removed outlier: 3.717A pdb=" N PHE D 147 " --> pdb=" O TRP D 154 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 53 through 55 290 hydrogen bonds defined for protein. 717 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: 6.26 Time building geometry restraints manager: 15.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9017 1.03 - 1.23: 30 1.23 - 1.42: 4009 1.42 - 1.62: 5295 1.62 - 1.81: 98 Bond restraints: 18449 Sorted by residual: bond pdb=" C TYR A 831 " pdb=" N PRO A 832 " ideal model delta sigma weight residual 1.326 1.342 -0.016 1.44e-02 4.82e+03 1.22e+00 bond pdb=" CB ARG A 889 " pdb=" CG ARG A 889 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.78e-01 bond pdb=" N PHE A 219 " pdb=" CA PHE A 219 " ideal model delta sigma weight residual 1.457 1.465 -0.008 1.10e-02 8.26e+03 4.70e-01 bond pdb=" CA ILE D 120 " pdb=" CB ILE D 120 " ideal model delta sigma weight residual 1.537 1.529 0.008 1.29e-02 6.01e+03 4.00e-01 bond pdb=" C ASN B 118 " pdb=" N ILE B 119 " ideal model delta sigma weight residual 1.338 1.331 0.006 1.05e-02 9.07e+03 3.74e-01 ... (remaining 18444 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.87: 257 106.87 - 113.64: 21571 113.64 - 120.41: 6266 120.41 - 127.19: 5014 127.19 - 133.96: 87 Bond angle restraints: 33195 Sorted by residual: angle pdb=" N ALA A 399 " pdb=" CA ALA A 399 " pdb=" C ALA A 399 " ideal model delta sigma weight residual 108.46 112.23 -3.77 1.51e+00 4.39e-01 6.23e+00 angle pdb=" N PRO A 339 " pdb=" CA PRO A 339 " pdb=" C PRO A 339 " ideal model delta sigma weight residual 110.21 113.54 -3.33 1.64e+00 3.72e-01 4.12e+00 angle pdb=" C ASN A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta sigma weight residual 121.54 125.17 -3.63 1.91e+00 2.74e-01 3.61e+00 angle pdb=" CA PRO B 183 " pdb=" C PRO B 183 " pdb=" O PRO B 183 " ideal model delta sigma weight residual 123.16 120.46 2.70 1.49e+00 4.50e-01 3.28e+00 angle pdb=" N LEU A 758 " pdb=" CA LEU A 758 " pdb=" C LEU A 758 " ideal model delta sigma weight residual 109.06 105.99 3.07 1.70e+00 3.46e-01 3.26e+00 ... (remaining 33190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 6862 17.11 - 34.22: 541 34.22 - 51.32: 85 51.32 - 68.43: 17 68.43 - 85.54: 7 Dihedral angle restraints: 7512 sinusoidal: 3418 harmonic: 4094 Sorted by residual: dihedral pdb=" CA ASP C 44 " pdb=" C ASP C 44 " pdb=" N THR C 45 " pdb=" CA THR C 45 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LYS C 43 " pdb=" C LYS C 43 " pdb=" N ASP C 44 " pdb=" CA ASP C 44 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN A 39 " pdb=" C ASN A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 887 0.027 - 0.054: 354 0.054 - 0.081: 103 0.081 - 0.107: 64 0.107 - 0.134: 31 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA VAL A 42 " pdb=" N VAL A 42 " pdb=" C VAL A 42 " pdb=" CB VAL A 42 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE G 91 " pdb=" N ILE G 91 " pdb=" C ILE G 91 " pdb=" CB ILE G 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE D 120 " pdb=" N ILE D 120 " pdb=" C ILE D 120 " pdb=" CB ILE D 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1436 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 726 " 0.153 9.50e-02 1.11e+02 5.12e-02 3.24e+00 pdb=" NE ARG A 726 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 726 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 726 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 726 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 726 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A 726 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 726 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 726 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 120 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 121 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 808 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 809 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 809 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 809 " -0.017 5.00e-02 4.00e+02 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 741 2.17 - 2.77: 35255 2.77 - 3.38: 49395 3.38 - 3.99: 63259 3.99 - 4.60: 99545 Nonbonded interactions: 248195 Sorted by model distance: nonbonded pdb=" OE1 GLN A 210 " pdb=" HH TYR A 237 " model vdw 1.556 1.850 nonbonded pdb=" O GLU A 144 " pdb=" HG1 THR A 148 " model vdw 1.587 1.850 nonbonded pdb=" OD2 ASP A 291 " pdb=" H ASN G 96 " model vdw 1.592 1.850 nonbonded pdb=" HG1 THR B 148 " pdb=" O ALA B 152 " model vdw 1.612 1.850 nonbonded pdb=" OD1 ASP D 161 " pdb=" H LYS D 165 " model vdw 1.616 1.850 ... (remaining 248190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.280 Extract box with map and model: 7.850 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 62.680 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9404 Z= 0.132 Angle : 0.453 5.784 12733 Z= 0.243 Chirality : 0.038 0.134 1439 Planarity : 0.003 0.067 1604 Dihedral : 13.346 85.539 3377 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1096 helix: 0.85 (0.26), residues: 456 sheet: -1.94 (0.50), residues: 111 loop : -1.36 (0.27), residues: 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.5040 time to fit residues: 108.1045 Evaluate side-chains 126 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN B 179 ASN D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9404 Z= 0.289 Angle : 0.538 5.951 12733 Z= 0.292 Chirality : 0.041 0.146 1439 Planarity : 0.004 0.045 1604 Dihedral : 4.239 23.622 1239 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.30 % Allowed : 5.52 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.25), residues: 1096 helix: 0.06 (0.24), residues: 468 sheet: -2.19 (0.46), residues: 120 loop : -1.43 (0.27), residues: 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 131 average time/residue: 0.4873 time to fit residues: 88.4465 Evaluate side-chains 119 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2212 time to fit residues: 3.0698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9404 Z= 0.149 Angle : 0.459 5.309 12733 Z= 0.245 Chirality : 0.039 0.144 1439 Planarity : 0.003 0.030 1604 Dihedral : 4.041 23.101 1239 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.26), residues: 1096 helix: 0.28 (0.25), residues: 465 sheet: -2.12 (0.44), residues: 127 loop : -1.19 (0.28), residues: 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.4656 time to fit residues: 80.3447 Evaluate side-chains 115 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2531 time to fit residues: 2.3382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 875 GLN D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9404 Z= 0.260 Angle : 0.506 5.347 12733 Z= 0.271 Chirality : 0.040 0.144 1439 Planarity : 0.004 0.031 1604 Dihedral : 4.211 24.380 1239 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.59 % Allowed : 7.59 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.25), residues: 1096 helix: 0.01 (0.25), residues: 463 sheet: -2.29 (0.46), residues: 117 loop : -1.33 (0.27), residues: 516 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 126 average time/residue: 0.5350 time to fit residues: 91.6236 Evaluate side-chains 120 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2038 time to fit residues: 3.7976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9404 Z= 0.180 Angle : 0.473 5.184 12733 Z= 0.251 Chirality : 0.039 0.143 1439 Planarity : 0.003 0.047 1604 Dihedral : 4.111 24.252 1239 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.10 % Allowed : 8.68 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.26), residues: 1096 helix: 0.17 (0.25), residues: 464 sheet: -2.21 (0.45), residues: 124 loop : -1.26 (0.27), residues: 508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.5221 time to fit residues: 89.3799 Evaluate side-chains 118 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2074 time to fit residues: 2.2634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9404 Z= 0.184 Angle : 0.469 5.115 12733 Z= 0.248 Chirality : 0.039 0.142 1439 Planarity : 0.003 0.038 1604 Dihedral : 4.050 24.114 1239 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.49 % Allowed : 8.97 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.26), residues: 1096 helix: 0.21 (0.25), residues: 464 sheet: -2.18 (0.46), residues: 124 loop : -1.25 (0.27), residues: 508 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 126 average time/residue: 0.4806 time to fit residues: 84.3689 Evaluate side-chains 121 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2149 time to fit residues: 2.8214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9404 Z= 0.187 Angle : 0.472 5.062 12733 Z= 0.249 Chirality : 0.039 0.140 1439 Planarity : 0.003 0.032 1604 Dihedral : 4.040 24.162 1239 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.10 % Allowed : 9.96 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1096 helix: 0.23 (0.25), residues: 464 sheet: -2.17 (0.46), residues: 124 loop : -1.25 (0.27), residues: 508 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.5242 time to fit residues: 92.0249 Evaluate side-chains 121 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2476 time to fit residues: 2.2587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 0.0270 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9404 Z= 0.305 Angle : 0.538 5.182 12733 Z= 0.289 Chirality : 0.041 0.141 1439 Planarity : 0.004 0.038 1604 Dihedral : 4.344 26.424 1239 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.30 % Allowed : 10.45 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.25), residues: 1096 helix: -0.12 (0.24), residues: 464 sheet: -2.32 (0.46), residues: 124 loop : -1.48 (0.27), residues: 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 125 average time/residue: 0.4677 time to fit residues: 81.8652 Evaluate side-chains 123 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2015 time to fit residues: 2.8744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9404 Z= 0.175 Angle : 0.479 5.051 12733 Z= 0.253 Chirality : 0.039 0.140 1439 Planarity : 0.003 0.029 1604 Dihedral : 4.161 25.720 1239 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.10 % Allowed : 10.75 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1096 helix: 0.12 (0.25), residues: 469 sheet: -2.23 (0.45), residues: 124 loop : -1.30 (0.28), residues: 503 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.4686 time to fit residues: 81.3195 Evaluate side-chains 119 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2425 time to fit residues: 2.2602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9404 Z= 0.202 Angle : 0.484 4.997 12733 Z= 0.257 Chirality : 0.039 0.139 1439 Planarity : 0.003 0.029 1604 Dihedral : 4.135 25.252 1239 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.30 % Allowed : 10.45 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.26), residues: 1096 helix: 0.12 (0.25), residues: 470 sheet: -2.16 (0.46), residues: 124 loop : -1.31 (0.28), residues: 502 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 121 average time/residue: 0.5084 time to fit residues: 85.6516 Evaluate side-chains 122 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2035 time to fit residues: 3.0160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.114372 restraints weight = 39580.944| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.35 r_work: 0.3458 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9404 Z= 0.189 Angle : 0.480 4.969 12733 Z= 0.254 Chirality : 0.039 0.138 1439 Planarity : 0.003 0.029 1604 Dihedral : 4.107 25.197 1239 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.10 % Allowed : 10.75 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.26), residues: 1096 helix: 0.16 (0.25), residues: 470 sheet: -2.16 (0.46), residues: 124 loop : -1.27 (0.28), residues: 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4187.06 seconds wall clock time: 74 minutes 47.68 seconds (4487.68 seconds total)