Starting phenix.real_space_refine on Thu Mar 5 02:05:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7thm_25898/03_2026/7thm_25898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7thm_25898/03_2026/7thm_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/cci-nas-00/data/ceres_data/7thm_25898/03_2026/7thm_25898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7thm_25898/03_2026/7thm_25898.map" model { file = "/net/cci-nas-00/data/ceres_data/7thm_25898/03_2026/7thm_25898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7thm_25898/03_2026/7thm_25898.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.82, per 1000 atoms: 0.15 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 - 3.00 Amino acid : True - 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: 1.83 Conformation dependent library (CDL) restraints added in 536.4 milliseconds 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... Secondary structure from input PDB file: 51 helices and 15 sheets defined 46.9% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.853A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.568A pdb=" N ILE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 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 153 through 159 Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.108A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.685A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 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) removed outlier: 3.587A pdb=" N THR A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 248' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.884A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 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) Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.534A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.376A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.713A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.030A pdb=" N LYS A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.607A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 561 through 581 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 596 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.604A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.596A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 710 Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 767 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.826A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.761A pdb=" N CYS A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 891 removed outlier: 3.628A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) 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 924 removed outlier: 4.011A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 99 through 109 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 118 through 124 removed outlier: 4.054A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.655A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 8 through 17 removed outlier: 3.833A pdb=" N LEU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 41 removed outlier: 4.326A pdb=" N ASP C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 58 removed outlier: 3.726A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 100 through 111 removed outlier: 3.508A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.605A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id=AA2, 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=AA3, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 204 removed outlier: 6.814A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.553A pdb=" N VAL B 131 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 128 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.940A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 541 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 557 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 820 Processing sheet with id=AB3, 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=AB4, first strand: chain 'D' and resid 148 through 149 Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'G' and resid 53 through 55 365 hydrogen bonds defined for protein. 1008 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: 4.49 Time building geometry restraints manager: 2.50 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=" O POP A1004 " pdb=" P2 POP A1004 " ideal model delta sigma weight residual 1.661 1.610 0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" O POP A1004 " pdb=" P1 POP A1004 " ideal model delta sigma weight residual 1.660 1.610 0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" O1 POP A1004 " pdb=" P1 POP A1004 " ideal model delta sigma weight residual 1.531 1.509 0.022 2.00e-02 2.50e+03 1.25e+00 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=" O2 POP A1004 " pdb=" P1 POP A1004 " ideal model delta sigma weight residual 1.531 1.509 0.022 2.00e-02 2.50e+03 1.16e+00 ... (remaining 18444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 33182 3.78 - 7.55: 11 7.55 - 11.33: 1 11.33 - 15.10: 0 15.10 - 18.88: 1 Bond angle restraints: 33195 Sorted by residual: angle pdb=" P1 POP A1004 " pdb=" O POP A1004 " pdb=" P2 POP A1004 " ideal model delta sigma weight residual 139.66 120.78 18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" O POP A1004 " pdb=" P1 POP A1004 " pdb=" O2 POP A1004 " ideal model delta sigma weight residual 102.11 109.86 -7.75 3.00e+00 1.11e-01 6.68e+00 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=" O POP A1004 " pdb=" P2 POP A1004 " pdb=" O4 POP A1004 " ideal model delta sigma weight residual 102.05 108.54 -6.49 3.00e+00 1.11e-01 4.67e+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 ... (remaining 33190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 7924 17.11 - 34.22: 608 34.22 - 51.32: 136 51.32 - 68.43: 47 68.43 - 85.54: 7 Dihedral angle restraints: 8722 sinusoidal: 4628 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 8719 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: 690 2.17 - 2.77: 35198 2.77 - 3.38: 49354 3.38 - 3.99: 63149 3.99 - 4.60: 99431 Nonbonded interactions: 247822 Sorted by model distance: nonbonded pdb=" OE1 GLN A 210 " pdb=" HH TYR A 237 " model vdw 1.556 2.450 nonbonded pdb=" O GLU A 144 " pdb=" HG1 THR A 148 " model vdw 1.587 2.450 nonbonded pdb=" OD2 ASP A 291 " pdb=" H ASN G 96 " model vdw 1.592 2.450 nonbonded pdb=" HG1 THR B 148 " pdb=" O ALA B 152 " model vdw 1.612 2.450 nonbonded pdb=" OD1 ASP D 161 " pdb=" H LYS D 165 " model vdw 1.616 2.450 ... (remaining 247817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- 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 0.051 9412 Z= 0.103 Angle : 0.499 18.876 12739 Z= 0.253 Chirality : 0.038 0.134 1439 Planarity : 0.003 0.067 1604 Dihedral : 13.360 85.539 3381 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.000 ARG A 726 TYR 0.015 0.001 TYR A 788 PHE 0.010 0.001 PHE A 741 TRP 0.005 0.001 TRP A 800 HIS 0.001 0.000 HIS A 810 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9404) covalent geometry : angle 0.49790 (12733) hydrogen bonds : bond 0.18889 ( 365) hydrogen bonds : angle 7.05302 ( 1008) metal coordination : bond 0.00580 ( 8) metal coordination : angle 1.51151 ( 6) *********************** 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 to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.478 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: 0.7603 (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: 0.2355 time to fit residues: 50.8361 Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.1980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN D 157 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116442 restraints weight = 39397.653| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.41 r_work: 0.3494 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9412 Z= 0.170 Angle : 0.536 5.825 12739 Z= 0.289 Chirality : 0.041 0.142 1439 Planarity : 0.004 0.052 1604 Dihedral : 4.298 24.065 1243 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.20 % Allowed : 5.42 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.26), residues: 1096 helix: 0.58 (0.25), residues: 476 sheet: -2.22 (0.43), residues: 129 loop : -1.20 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 858 TYR 0.022 0.001 TYR A 887 PHE 0.012 0.001 PHE A 471 TRP 0.007 0.001 TRP G 53 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9404) covalent geometry : angle 0.53369 (12733) hydrogen bonds : bond 0.05030 ( 365) hydrogen bonds : angle 5.40443 ( 1008) metal coordination : bond 0.01077 ( 8) metal coordination : angle 2.30824 ( 6) *********************** 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 to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.549 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: 0.8937 (mptt) cc_final: 0.8592 (mmtp) REVERT: D 111 ARG cc_start: 0.4733 (mmm160) cc_final: 0.4139 (mmp-170) outliers start: 2 outliers final: 2 residues processed: 130 average time/residue: 0.2397 time to fit residues: 42.6547 Evaluate side-chains 122 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 VAL 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 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 65 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN G 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.142506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116052 restraints weight = 39851.711| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.42 r_work: 0.3494 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9412 Z= 0.157 Angle : 0.507 5.431 12739 Z= 0.273 Chirality : 0.040 0.145 1439 Planarity : 0.003 0.038 1604 Dihedral : 4.330 24.854 1243 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.39 % Allowed : 6.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.26), residues: 1096 helix: 0.53 (0.25), residues: 478 sheet: -2.31 (0.43), residues: 126 loop : -1.17 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 858 TYR 0.012 0.001 TYR A 788 PHE 0.017 0.001 PHE A 471 TRP 0.005 0.001 TRP A 216 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9404) covalent geometry : angle 0.50583 (12733) hydrogen bonds : bond 0.04287 ( 365) hydrogen bonds : angle 5.06106 ( 1008) metal coordination : bond 0.00879 ( 8) metal coordination : angle 1.93615 ( 6) *********************** 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 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.514 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: 0.8938 (mptt) cc_final: 0.8589 (mmtp) REVERT: D 99 ASP cc_start: 0.8126 (t70) cc_final: 0.7667 (t0) REVERT: D 111 ARG cc_start: 0.4658 (mmm160) cc_final: 0.4152 (mmp-170) REVERT: D 127 LYS cc_start: 0.7604 (ptmm) cc_final: 0.7391 (ptmm) outliers start: 4 outliers final: 2 residues processed: 133 average time/residue: 0.2534 time to fit residues: 45.6343 Evaluate side-chains 125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.143558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117301 restraints weight = 39393.214| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.39 r_work: 0.3508 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.123 Angle : 0.482 5.204 12739 Z= 0.258 Chirality : 0.039 0.143 1439 Planarity : 0.003 0.043 1604 Dihedral : 4.206 24.615 1243 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.20 % Allowed : 8.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 1096 helix: 0.67 (0.25), residues: 479 sheet: -2.07 (0.45), residues: 123 loop : -1.14 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 111 TYR 0.015 0.001 TYR A 887 PHE 0.019 0.001 PHE A 471 TRP 0.004 0.001 TRP B 154 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9404) covalent geometry : angle 0.48103 (12733) hydrogen bonds : bond 0.03641 ( 365) hydrogen bonds : angle 4.73340 ( 1008) metal coordination : bond 0.00676 ( 8) metal coordination : angle 1.71912 ( 6) *********************** 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 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.486 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: 0.8924 (mptt) cc_final: 0.8577 (mmtp) REVERT: A 794 MET cc_start: 0.7845 (ttp) cc_final: 0.7580 (ttp) REVERT: A 818 MET cc_start: 0.6787 (ptm) cc_final: 0.6449 (ptm) REVERT: C 49 PHE cc_start: 0.6517 (m-80) cc_final: 0.6235 (m-80) REVERT: D 99 ASP cc_start: 0.8078 (t70) cc_final: 0.7750 (t0) REVERT: D 111 ARG cc_start: 0.5005 (mmm160) cc_final: 0.4155 (mmp-170) outliers start: 2 outliers final: 2 residues processed: 132 average time/residue: 0.2370 time to fit residues: 42.4390 Evaluate side-chains 125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115990 restraints weight = 39731.687| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.31 r_work: 0.3483 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9412 Z= 0.175 Angle : 0.520 5.366 12739 Z= 0.279 Chirality : 0.040 0.144 1439 Planarity : 0.004 0.029 1604 Dihedral : 4.357 26.357 1243 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.59 % Allowed : 9.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.26), residues: 1096 helix: 0.55 (0.25), residues: 478 sheet: -2.08 (0.44), residues: 128 loop : -1.27 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.013 0.001 TYR A 788 PHE 0.021 0.001 PHE A 471 TRP 0.007 0.001 TRP A 216 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9404) covalent geometry : angle 0.51766 (12733) hydrogen bonds : bond 0.03956 ( 365) hydrogen bonds : angle 4.80746 ( 1008) metal coordination : bond 0.01012 ( 8) metal coordination : angle 2.08834 ( 6) *********************** 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 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.457 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: 0.8960 (mptt) cc_final: 0.8614 (mmtp) REVERT: A 818 MET cc_start: 0.6744 (ptm) cc_final: 0.6433 (ptm) REVERT: C 49 PHE cc_start: 0.6301 (m-80) cc_final: 0.5941 (m-80) REVERT: D 99 ASP cc_start: 0.8193 (t70) cc_final: 0.7903 (t0) outliers start: 6 outliers final: 3 residues processed: 132 average time/residue: 0.2163 time to fit residues: 39.9688 Evaluate side-chains 123 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.142449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116443 restraints weight = 39381.509| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.37 r_work: 0.3500 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.129 Angle : 0.486 5.167 12739 Z= 0.259 Chirality : 0.039 0.141 1439 Planarity : 0.003 0.028 1604 Dihedral : 4.251 26.176 1243 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.69 % Allowed : 9.96 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 1096 helix: 0.70 (0.25), residues: 478 sheet: -2.04 (0.45), residues: 123 loop : -1.17 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.012 0.001 TYR A 788 PHE 0.019 0.001 PHE A 471 TRP 0.004 0.001 TRP B 154 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9404) covalent geometry : angle 0.48478 (12733) hydrogen bonds : bond 0.03491 ( 365) hydrogen bonds : angle 4.61139 ( 1008) metal coordination : bond 0.00803 ( 8) metal coordination : angle 1.73452 ( 6) *********************** 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 130 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8969 (mptt) cc_final: 0.8616 (mmtp) REVERT: A 818 MET cc_start: 0.6757 (ptm) cc_final: 0.6475 (ptm) REVERT: C 49 PHE cc_start: 0.6299 (m-80) cc_final: 0.5957 (m-80) REVERT: D 99 ASP cc_start: 0.8135 (t70) cc_final: 0.7887 (t0) outliers start: 7 outliers final: 7 residues processed: 128 average time/residue: 0.2184 time to fit residues: 38.9329 Evaluate side-chains 127 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.144477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119214 restraints weight = 39618.195| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.31 r_work: 0.3520 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9412 Z= 0.107 Angle : 0.467 5.020 12739 Z= 0.248 Chirality : 0.039 0.141 1439 Planarity : 0.003 0.028 1604 Dihedral : 4.119 25.091 1243 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.79 % Allowed : 10.55 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.26), residues: 1096 helix: 0.86 (0.25), residues: 478 sheet: -1.98 (0.46), residues: 123 loop : -1.07 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.011 0.001 TYR A 788 PHE 0.020 0.001 PHE A 471 TRP 0.004 0.001 TRP B 154 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9404) covalent geometry : angle 0.46608 (12733) hydrogen bonds : bond 0.03159 ( 365) hydrogen bonds : angle 4.43045 ( 1008) metal coordination : bond 0.00626 ( 8) metal coordination : angle 1.48691 ( 6) *********************** 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 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8924 (mptt) cc_final: 0.8592 (mmtp) REVERT: A 794 MET cc_start: 0.7807 (ttp) cc_final: 0.7565 (ttp) REVERT: A 818 MET cc_start: 0.6712 (ptm) cc_final: 0.6431 (ptm) REVERT: C 49 PHE cc_start: 0.6642 (m-80) cc_final: 0.6362 (m-80) REVERT: D 99 ASP cc_start: 0.8082 (t70) cc_final: 0.7872 (t0) outliers start: 8 outliers final: 6 residues processed: 130 average time/residue: 0.2312 time to fit residues: 41.8220 Evaluate side-chains 129 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.145257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120489 restraints weight = 39330.165| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.29 r_work: 0.3605 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9412 Z= 0.105 Angle : 0.468 5.129 12739 Z= 0.247 Chirality : 0.039 0.139 1439 Planarity : 0.003 0.028 1604 Dihedral : 4.061 24.678 1243 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.69 % Allowed : 10.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.26), residues: 1096 helix: 0.94 (0.25), residues: 476 sheet: -1.91 (0.44), residues: 133 loop : -1.06 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.011 0.001 TYR A 788 PHE 0.017 0.001 PHE A 471 TRP 0.004 0.001 TRP A 290 HIS 0.002 0.000 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9404) covalent geometry : angle 0.46661 (12733) hydrogen bonds : bond 0.03055 ( 365) hydrogen bonds : angle 4.36623 ( 1008) metal coordination : bond 0.00580 ( 8) metal coordination : angle 1.47110 ( 6) *********************** 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 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8889 (mptt) cc_final: 0.8577 (mmtp) REVERT: A 426 LYS cc_start: 0.8062 (mptt) cc_final: 0.7840 (mptt) REVERT: A 794 MET cc_start: 0.7784 (ttp) cc_final: 0.7554 (ttp) REVERT: A 818 MET cc_start: 0.6892 (ptm) cc_final: 0.6625 (ptm) REVERT: C 49 PHE cc_start: 0.6611 (m-80) cc_final: 0.6390 (m-80) outliers start: 7 outliers final: 7 residues processed: 130 average time/residue: 0.2523 time to fit residues: 44.6144 Evaluate side-chains 128 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.142839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117168 restraints weight = 39473.984| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.36 r_work: 0.3500 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.136 Angle : 0.487 5.073 12739 Z= 0.258 Chirality : 0.040 0.139 1439 Planarity : 0.003 0.029 1604 Dihedral : 4.139 25.482 1243 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.89 % Allowed : 11.05 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.26), residues: 1096 helix: 0.86 (0.25), residues: 476 sheet: -1.94 (0.45), residues: 126 loop : -1.12 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 96 TYR 0.012 0.001 TYR A 788 PHE 0.017 0.001 PHE A 471 TRP 0.005 0.001 TRP A 216 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9404) covalent geometry : angle 0.48608 (12733) hydrogen bonds : bond 0.03280 ( 365) hydrogen bonds : angle 4.43653 ( 1008) metal coordination : bond 0.00842 ( 8) metal coordination : angle 1.70960 ( 6) *********************** 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 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8910 (mptt) cc_final: 0.8575 (mmtp) REVERT: A 426 LYS cc_start: 0.8070 (mptt) cc_final: 0.7833 (mptt) REVERT: A 818 MET cc_start: 0.6856 (ptm) cc_final: 0.6598 (ptm) REVERT: B 111 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.6820 (ttp-170) REVERT: C 49 PHE cc_start: 0.6579 (m-80) cc_final: 0.6277 (m-80) outliers start: 9 outliers final: 9 residues processed: 130 average time/residue: 0.2508 time to fit residues: 44.3751 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP 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 C residue 36 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 127 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.144098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119139 restraints weight = 39616.718| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.27 r_work: 0.3514 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.117 Angle : 0.476 4.969 12739 Z= 0.252 Chirality : 0.039 0.139 1439 Planarity : 0.003 0.029 1604 Dihedral : 4.098 25.385 1243 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.89 % Allowed : 11.44 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.26), residues: 1096 helix: 0.92 (0.25), residues: 476 sheet: -1.94 (0.45), residues: 126 loop : -1.08 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.011 0.001 TYR A 788 PHE 0.017 0.001 PHE A 471 TRP 0.004 0.001 TRP B 154 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9404) covalent geometry : angle 0.47483 (12733) hydrogen bonds : bond 0.03129 ( 365) hydrogen bonds : angle 4.35528 ( 1008) metal coordination : bond 0.00708 ( 8) metal coordination : angle 1.51900 ( 6) ********************** 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 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8852 (mptt) cc_final: 0.8554 (mmtp) REVERT: A 426 LYS cc_start: 0.8040 (mptt) cc_final: 0.7804 (mptt) REVERT: A 794 MET cc_start: 0.7834 (ttp) cc_final: 0.7588 (ttp) REVERT: A 818 MET cc_start: 0.6827 (ptm) cc_final: 0.6561 (ptm) REVERT: B 111 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.6820 (ttp-170) REVERT: C 49 PHE cc_start: 0.6516 (m-80) cc_final: 0.6245 (m-80) REVERT: D 127 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6968 (tmtt) REVERT: D 168 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6058 (pp30) outliers start: 9 outliers final: 7 residues processed: 131 average time/residue: 0.2401 time to fit residues: 42.7405 Evaluate side-chains 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP 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 C residue 36 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 127 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 112 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.144855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.119874 restraints weight = 39418.462| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.29 r_work: 0.3608 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9412 Z= 0.107 Angle : 0.469 5.460 12739 Z= 0.248 Chirality : 0.039 0.138 1439 Planarity : 0.003 0.028 1604 Dihedral : 4.033 24.935 1243 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.69 % Allowed : 11.64 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.26), residues: 1096 helix: 1.01 (0.25), residues: 475 sheet: -1.91 (0.44), residues: 127 loop : -0.99 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.011 0.001 TYR A 788 PHE 0.016 0.001 PHE A 471 TRP 0.004 0.001 TRP B 154 HIS 0.002 0.000 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9404) covalent geometry : angle 0.46851 (12733) hydrogen bonds : bond 0.02974 ( 365) hydrogen bonds : angle 4.28124 ( 1008) metal coordination : bond 0.00594 ( 8) metal coordination : angle 1.40182 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4583.61 seconds wall clock time: 78 minutes 25.57 seconds (4705.57 seconds total)