Starting phenix.real_space_refine on Sun Mar 17 15:43:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/03_2024/7thm_25898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/03_2024/7thm_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_25898/03_2024/7thm_25898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/03_2024/7thm_25898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/03_2024/7thm_25898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thm_25898/03_2024/7thm_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-dev-5265/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: 7.79, per 1000 atoms: 0.43 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: 13.19 Conformation dependent library (CDL) restraints added in 1.6 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: 3.13 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: 6.03 Time building geometry restraints manager: 13.77 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: 7923 17.11 - 34.22: 605 34.22 - 51.32: 136 51.32 - 68.43: 47 68.43 - 85.54: 7 Dihedral angle restraints: 8718 sinusoidal: 4624 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 8715 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: 1.590 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: 0.260 Extract box with map and model: 7.820 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 59.520 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.610 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 800 HIS 0.001 0.000 HIS A 810 PHE 0.010 0.001 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.010 0.000 ARG A 726 *********************** 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 : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 101 ASP cc_start: 0.7829 (p0) cc_final: 0.7602 (p0) REVERT: D 111 ARG cc_start: 0.4633 (mmm160) cc_final: 0.4131 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.4958 time to fit residues: 106.5722 Evaluate side-chains 127 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.7393 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9404 Z= 0.338 Angle : 0.572 6.384 12733 Z= 0.311 Chirality : 0.042 0.142 1439 Planarity : 0.005 0.047 1604 Dihedral : 4.422 24.849 1239 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.30 % Allowed : 6.02 % Favored : 93.69 % 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: -1.52 (0.25), residues: 1096 helix: -0.09 (0.24), residues: 466 sheet: -2.02 (0.50), residues: 103 loop : -1.60 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 216 HIS 0.005 0.001 HIS A 99 PHE 0.015 0.002 PHE A 753 TYR 0.018 0.002 TYR A 887 ARG 0.004 0.001 ARG A 640 *********************** 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 130 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8693 (mptt) cc_final: 0.8418 (mmtp) REVERT: D 101 ASP cc_start: 0.7595 (p0) cc_final: 0.7384 (p0) REVERT: D 111 ARG cc_start: 0.4582 (mmm160) cc_final: 0.4122 (mmp-170) outliers start: 3 outliers final: 3 residues processed: 129 average time/residue: 0.5272 time to fit residues: 92.4639 Evaluate side-chains 121 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.0030 chunk 31 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 82 optimal weight: 0.0870 overall best weight: 0.3166 ------------------------------------------------------------------------------- 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: 0.7315 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9404 Z= 0.130 Angle : 0.459 5.341 12733 Z= 0.246 Chirality : 0.038 0.144 1439 Planarity : 0.003 0.041 1604 Dihedral : 4.089 23.482 1239 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.20 % Allowed : 6.80 % Favored : 93.00 % 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: -1.11 (0.26), residues: 1096 helix: 0.24 (0.25), residues: 466 sheet: -2.26 (0.45), residues: 124 loop : -1.18 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 53 HIS 0.002 0.000 HIS C 36 PHE 0.015 0.001 PHE A 471 TYR 0.011 0.001 TYR A 788 ARG 0.007 0.000 ARG B 111 *********************** 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 127 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 101 ASP cc_start: 0.7532 (p0) cc_final: 0.7325 (p0) REVERT: D 111 ARG cc_start: 0.4553 (mmm160) cc_final: 0.4194 (mmp-170) outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 0.4756 time to fit residues: 82.6562 Evaluate side-chains 121 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 875 GLN 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: 0.7421 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9404 Z= 0.364 Angle : 0.570 5.603 12733 Z= 0.309 Chirality : 0.042 0.150 1439 Planarity : 0.004 0.042 1604 Dihedral : 4.516 26.982 1239 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.79 % Allowed : 8.28 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.25), residues: 1096 helix: -0.38 (0.24), residues: 465 sheet: -2.43 (0.46), residues: 117 loop : -1.60 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 216 HIS 0.008 0.001 HIS A 99 PHE 0.019 0.002 PHE A 471 TYR 0.013 0.002 TYR A 788 ARG 0.005 0.001 ARG A 640 *********************** 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: 8 poor density : 120 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8788 (mptt) cc_final: 0.8508 (mmtp) REVERT: A 818 MET cc_start: 0.6978 (ptm) cc_final: 0.6683 (ptm) REVERT: D 101 ASP cc_start: 0.7590 (p0) cc_final: 0.7366 (p0) outliers start: 8 outliers final: 6 residues processed: 126 average time/residue: 0.5090 time to fit residues: 87.5240 Evaluate side-chains 123 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 105 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7377 moved from start: 0.1546 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= 0.200 Angle : 0.489 5.407 12733 Z= 0.262 Chirality : 0.040 0.144 1439 Planarity : 0.003 0.029 1604 Dihedral : 4.326 26.930 1239 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.89 % Allowed : 9.17 % 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: -1.52 (0.25), residues: 1096 helix: -0.11 (0.24), residues: 462 sheet: -2.38 (0.45), residues: 126 loop : -1.41 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 216 HIS 0.003 0.001 HIS A 99 PHE 0.020 0.001 PHE A 471 TYR 0.011 0.001 TYR A 788 ARG 0.002 0.000 ARG B 111 *********************** 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 128 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8760 (mptt) cc_final: 0.8468 (mmtp) REVERT: A 818 MET cc_start: 0.6954 (ptm) cc_final: 0.6700 (ptm) outliers start: 9 outliers final: 8 residues processed: 122 average time/residue: 0.4817 time to fit residues: 82.2763 Evaluate side-chains 126 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 105 ASN 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: 2.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.7407 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9404 Z= 0.283 Angle : 0.525 5.414 12733 Z= 0.282 Chirality : 0.041 0.145 1439 Planarity : 0.004 0.033 1604 Dihedral : 4.420 27.688 1239 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 1.08 % Allowed : 10.36 % Favored : 88.56 % 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: -1.74 (0.25), residues: 1096 helix: -0.28 (0.24), residues: 463 sheet: -2.45 (0.43), residues: 136 loop : -1.54 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 216 HIS 0.006 0.001 HIS A 99 PHE 0.022 0.001 PHE A 471 TYR 0.013 0.001 TYR A 788 ARG 0.003 0.000 ARG A 640 *********************** 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 134 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8788 (mptt) cc_final: 0.8491 (mmtp) REVERT: A 818 MET cc_start: 0.6953 (ptm) cc_final: 0.6704 (ptm) outliers start: 11 outliers final: 8 residues processed: 128 average time/residue: 0.4968 time to fit residues: 89.1374 Evaluate side-chains 129 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 105 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 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: 0.2980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7372 moved from start: 0.1701 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= 0.185 Angle : 0.478 5.280 12733 Z= 0.255 Chirality : 0.039 0.141 1439 Planarity : 0.003 0.030 1604 Dihedral : 4.247 26.968 1239 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.89 % Allowed : 10.85 % Favored : 88.26 % 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: -1.38 (0.25), residues: 1096 helix: 0.01 (0.25), residues: 464 sheet: -2.30 (0.45), residues: 124 loop : -1.35 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 154 HIS 0.003 0.001 HIS A 99 PHE 0.020 0.001 PHE A 471 TYR 0.011 0.001 TYR A 788 ARG 0.002 0.000 ARG B 111 *********************** 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 131 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8678 (mptt) cc_final: 0.8456 (mmtp) REVERT: A 794 MET cc_start: 0.7742 (ttp) cc_final: 0.7533 (ttp) REVERT: A 818 MET cc_start: 0.6940 (ptm) cc_final: 0.6696 (ptm) outliers start: 9 outliers final: 8 residues processed: 126 average time/residue: 0.4717 time to fit residues: 82.4459 Evaluate side-chains 127 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 105 ASN 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: 0.9980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 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: 0.7415 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9404 Z= 0.302 Angle : 0.530 5.341 12733 Z= 0.285 Chirality : 0.041 0.143 1439 Planarity : 0.004 0.035 1604 Dihedral : 4.417 28.157 1239 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 1.58 % Allowed : 10.95 % Favored : 87.48 % 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: -1.70 (0.25), residues: 1096 helix: -0.29 (0.24), residues: 462 sheet: -2.38 (0.45), residues: 124 loop : -1.52 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 216 HIS 0.005 0.001 HIS A 99 PHE 0.020 0.001 PHE A 471 TYR 0.013 0.001 TYR A 788 ARG 0.003 0.000 ARG A 640 *********************** 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 137 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8698 (mptt) cc_final: 0.8475 (mmtp) REVERT: A 794 MET cc_start: 0.7750 (ttp) cc_final: 0.7524 (ttp) REVERT: A 818 MET cc_start: 0.6998 (ptm) cc_final: 0.6765 (ptm) outliers start: 16 outliers final: 13 residues processed: 130 average time/residue: 0.4978 time to fit residues: 88.0114 Evaluate side-chains 130 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain G residue 13 SER 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: 5.9990 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7366 moved from start: 0.1818 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= 0.173 Angle : 0.473 5.109 12733 Z= 0.251 Chirality : 0.039 0.140 1439 Planarity : 0.004 0.064 1604 Dihedral : 4.201 26.714 1239 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.79 % Allowed : 11.74 % Favored : 87.48 % 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: -1.33 (0.26), residues: 1096 helix: 0.04 (0.25), residues: 464 sheet: -2.28 (0.46), residues: 124 loop : -1.30 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 154 HIS 0.003 0.001 HIS A 928 PHE 0.019 0.001 PHE A 471 TYR 0.010 0.001 TYR A 788 ARG 0.012 0.000 ARG B 111 *********************** 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 130 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8679 (mptt) cc_final: 0.8446 (mmtp) REVERT: A 794 MET cc_start: 0.7701 (ttp) cc_final: 0.7501 (ttp) REVERT: A 818 MET cc_start: 0.6930 (ptm) cc_final: 0.6695 (ptm) REVERT: D 168 GLN cc_start: 0.6704 (tm-30) cc_final: 0.5816 (pp30) outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.4912 time to fit residues: 86.5572 Evaluate side-chains 126 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain D residue 105 ASN 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: 0.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7380 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 0.025 9404 Z= 0.205 Angle : 0.484 5.128 12733 Z= 0.258 Chirality : 0.039 0.139 1439 Planarity : 0.004 0.055 1604 Dihedral : 4.185 26.511 1239 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.89 % Allowed : 11.83 % Favored : 87.28 % 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: 0.02 (0.25), residues: 464 sheet: -2.30 (0.45), residues: 124 loop : -1.34 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 216 HIS 0.004 0.001 HIS A 99 PHE 0.020 0.001 PHE A 471 TYR 0.011 0.001 TYR A 788 ARG 0.007 0.000 ARG B 111 ********************** 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 132 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8696 (mptt) cc_final: 0.8465 (mmtp) REVERT: A 794 MET cc_start: 0.7739 (ttp) cc_final: 0.7530 (ttp) REVERT: A 818 MET cc_start: 0.6949 (ptm) cc_final: 0.6707 (ptm) REVERT: D 168 GLN cc_start: 0.6690 (tm-30) cc_final: 0.5779 (pp30) outliers start: 9 outliers final: 9 residues processed: 127 average time/residue: 0.4769 time to fit residues: 83.5563 Evaluate side-chains 127 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain D residue 105 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.7980 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: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 64 optimal weight: 0.9980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.142470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116809 restraints weight = 39613.560| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.30 r_work: 0.3484 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.003 0.024 9404 Z= 0.176 Angle : 0.473 5.064 12733 Z= 0.251 Chirality : 0.039 0.138 1439 Planarity : 0.003 0.055 1604 Dihedral : 4.142 26.218 1239 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.99 % Allowed : 12.13 % Favored : 86.88 % 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: -1.22 (0.26), residues: 1096 helix: 0.13 (0.25), residues: 465 sheet: -2.26 (0.45), residues: 125 loop : -1.24 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 154 HIS 0.003 0.001 HIS A 99 PHE 0.020 0.001 PHE A 471 TYR 0.010 0.001 TYR A 788 ARG 0.008 0.000 ARG B 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4390.47 seconds wall clock time: 77 minutes 54.36 seconds (4674.36 seconds total)