Starting phenix.real_space_refine on Sat Oct 24 01:58:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30sj_57999/10_2026/30sj_57999.cif Found real_map, /net/cci-nas-00/data/ceres_data/30sj_57999/10_2026/30sj_57999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30sj_57999/10_2026/30sj_57999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30sj_57999/10_2026/30sj_57999.map" model { file = "/net/cci-nas-00/data/ceres_data/30sj_57999/10_2026/30sj_57999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30sj_57999/10_2026/30sj_57999.cif" } resolution = 3.2 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= 0.005 sd= 0.030 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 Ca 2 9.91 5 Fe 4 7.16 5 Cu 2 5.60 5 P 1 5.49 5 S 44 5.16 5 C 7738 2.51 5 N 1925 2.21 5 O 1966 1.98 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11682 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5684 Classifications: {'peptide': 718} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 683} Chain breaks: 1 Chain: "B" Number of atoms: 5705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5705 Classifications: {'peptide': 720} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 685} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {' CA': 1, ' CU': 1, 'HEM': 2, 'LMO': 1, 'LOP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 123 Unusual residues: {' CA': 1, ' CU': 1, 'HEM': 2, 'LMO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.83, per 1000 atoms: 0.24 Number of scatterers: 11682 At special positions: 0 Unit cell: (104.65, 100.1, 105.95, 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) Cu 2 28.99 Fe 4 26.01 Ca 2 19.99 S 44 16.00 P 1 15.00 O 1966 8.00 N 1925 7.00 C 7738 6.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 490.5 milliseconds 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2614 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 78.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.844A pdb=" N GLY A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 65 removed outlier: 3.517A pdb=" N GLY A 65 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.525A pdb=" N LEU A 111 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.811A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 254 Processing helix chain 'A' and resid 268 through 272 removed outlier: 3.953A pdb=" N THR A 272 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 307 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 323 through 355 Proline residue: A 352 - end of helix removed outlier: 3.980A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.602A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'A' and resid 512 through 537 removed outlier: 5.019A pdb=" N ILE A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) Proline residue: A 533 - end of helix Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.668A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.755A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.508A pdb=" N LEU A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.309A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 3.538A pdb=" N VAL A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 681 Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 720 Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'B' and resid 5 through 33 removed outlier: 3.522A pdb=" N GLY B 27 " --> pdb=" O GLY B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 removed outlier: 3.573A pdb=" N GLY B 65 " --> pdb=" O TRP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 82 through 104 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.543A pdb=" N LEU B 111 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.773A pdb=" N ALA B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 142 through 161 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 240 through 253 Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.820A pdb=" N THR B 272 " --> pdb=" O PRO B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.551A pdb=" N GLN B 320 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 355 Proline residue: B 352 - end of helix removed outlier: 4.087A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 439 Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 473 through 489 Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 512 through 537 removed outlier: 5.078A pdb=" N ILE B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Proline residue: B 533 - end of helix Processing helix chain 'B' and resid 545 through 553 removed outlier: 3.571A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 586 through 606 removed outlier: 3.555A pdb=" N LEU B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.321A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.859A pdb=" N PHE B 635 " --> pdb=" O HIS B 631 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 654 Processing helix chain 'B' and resid 660 through 681 Processing helix chain 'B' and resid 682 through 697 Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 719 Processing helix chain 'B' and resid 719 through 744 removed outlier: 4.592A pdb=" N GLY B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.531A pdb=" N ALA B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.738A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.723A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 785 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 3633 1.36 - 1.54: 8127 1.54 - 1.71: 217 1.71 - 1.88: 84 1.88 - 2.06: 16 Bond restraints: 12077 Sorted by residual: bond pdb=" N VAL B 238 " pdb=" CA VAL B 238 " ideal model delta sigma weight residual 1.458 1.503 -0.046 1.41e-02 5.03e+03 1.05e+01 bond pdb=" N VAL B 239 " pdb=" CA VAL B 239 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.29e-02 6.01e+03 8.95e+00 bond pdb=" CA ALA B 242 " pdb=" CB ALA B 242 " ideal model delta sigma weight residual 1.531 1.485 0.046 1.59e-02 3.96e+03 8.36e+00 bond pdb=" O2 LOP A 805 " pdb=" P1 LOP A 805 " ideal model delta sigma weight residual 1.650 1.600 0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C VAL B 239 " pdb=" O VAL B 239 " ideal model delta sigma weight residual 1.240 1.203 0.037 1.49e-02 4.50e+03 6.07e+00 ... (remaining 12072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 16341 2.41 - 4.81: 147 4.81 - 7.22: 26 7.22 - 9.63: 4 9.63 - 12.03: 4 Bond angle restraints: 16522 Sorted by residual: angle pdb=" N LEU B 240 " pdb=" CA LEU B 240 " pdb=" C LEU B 240 " ideal model delta sigma weight residual 113.97 105.89 8.08 1.28e+00 6.10e-01 3.98e+01 angle pdb=" N VAL B 239 " pdb=" CA VAL B 239 " pdb=" C VAL B 239 " ideal model delta sigma weight residual 112.90 107.14 5.76 9.60e-01 1.09e+00 3.60e+01 angle pdb=" N LEU B 241 " pdb=" CA LEU B 241 " pdb=" C LEU B 241 " ideal model delta sigma weight residual 113.18 106.11 7.07 1.21e+00 6.83e-01 3.41e+01 angle pdb=" N ALA B 242 " pdb=" CA ALA B 242 " pdb=" C ALA B 242 " ideal model delta sigma weight residual 112.45 105.20 7.25 1.39e+00 5.18e-01 2.72e+01 angle pdb=" CA GLN A 737 " pdb=" CB GLN A 737 " pdb=" CG GLN A 737 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.23e+00 ... (remaining 16517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5907 17.83 - 35.66: 657 35.66 - 53.49: 196 53.49 - 71.32: 39 71.32 - 89.16: 17 Dihedral angle restraints: 6816 sinusoidal: 2715 harmonic: 4101 Sorted by residual: dihedral pdb=" CA ILE B 679 " pdb=" C ILE B 679 " pdb=" N PHE B 680 " pdb=" CA PHE B 680 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ILE A 679 " pdb=" C ILE A 679 " pdb=" N PHE A 680 " pdb=" CA PHE A 680 " ideal model delta harmonic sigma weight residual 180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C2D HEM A 802 " pdb=" C3D HEM A 802 " pdb=" CAD HEM A 802 " pdb=" CBD HEM A 802 " ideal model delta sinusoidal sigma weight residual 180.00 90.84 89.16 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 6813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1589 0.062 - 0.125: 156 0.125 - 0.187: 5 0.187 - 0.249: 0 0.249 - 0.311: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" C4 LOP A 805 " pdb=" C3 LOP A 805 " pdb=" C5 LOP A 805 " pdb=" O5 LOP A 805 " both_signs ideal model delta sigma weight residual False -2.34 -2.65 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL B 238 " pdb=" CA VAL B 238 " pdb=" CG1 VAL B 238 " pdb=" CG2 VAL B 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA THR A 546 " pdb=" N THR A 546 " pdb=" C THR A 546 " pdb=" CB THR A 546 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 1749 not shown) Planarity restraints: 2037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 LOP A 805 " -0.085 2.00e-02 2.50e+03 1.70e-01 2.88e+02 pdb=" C14 LOP A 805 " 0.225 2.00e-02 2.50e+03 pdb=" C15 LOP A 805 " -0.224 2.00e-02 2.50e+03 pdb=" C16 LOP A 805 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 571 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C TRP B 571 " -0.048 2.00e-02 2.50e+03 pdb=" O TRP B 571 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B 572 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 569 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C GLU B 569 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU B 569 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 570 " -0.014 2.00e-02 2.50e+03 ... (remaining 2034 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 175 2.67 - 3.23: 10991 3.23 - 3.79: 19873 3.79 - 4.34: 25787 4.34 - 4.90: 44087 Nonbonded interactions: 100913 Sorted by model distance: nonbonded pdb=" NE2 HIS A 217 " pdb="CU CU A 804 " model vdw 2.114 2.320 nonbonded pdb=" NE2 HIS B 217 " pdb="CU CU B 805 " model vdw 2.115 2.320 nonbonded pdb=" ND1 HIS B 224 " pdb="CU CU B 805 " model vdw 2.145 2.320 nonbonded pdb=" ND1 HIS A 224 " pdb="CU CU A 804 " model vdw 2.148 2.320 nonbonded pdb=" OE1 GLN B 62 " pdb=" OH TYR B 406 " model vdw 2.221 3.040 ... (remaining 100908 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 200 or (resid 201 and (name N or name CA or name \ C or name O )) or resid 202 through 466 or resid 468 through 524 or (resid 525 \ and (name N or name CA or name C or name O or name CB )) or resid 526 through 75 \ 0 or resid 802)) selection = (chain 'B' and (resid 7 through 750 or resid 802)) } 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.490 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12081 Z= 0.145 Angle : 0.571 12.032 16522 Z= 0.275 Chirality : 0.037 0.311 1752 Planarity : 0.005 0.170 2037 Dihedral : 16.999 89.156 4202 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.65 % Allowed : 19.36 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.03 (0.23), residues: 1430 helix: 2.24 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -0.74 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 575 TYR 0.011 0.001 TYR A 479 PHE 0.008 0.001 PHE A 635 TRP 0.016 0.001 TRP B 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (12077) covalent geometry : angle 0.57102 / 0.28 (16522) hydrogen bonds : bond 0.12563 / 8.25 ( 785) hydrogen bonds : angle 4.62621 / 3.41 ( 2274) Misc. bond : bond 0.05405 / 2.72 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6594 (ppt170) REVERT: B 178 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7826 (t0) outliers start: 30 outliers final: 9 residues processed: 141 average time/residue: 0.0849 time to fit residues: 18.6092 Evaluate side-chains 92 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.052578 restraints weight = 49579.420| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.75 r_work: 0.2836 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.206 12081 Z= 0.132 Angle : 0.569 8.384 16522 Z= 0.266 Chirality : 0.038 0.161 1752 Planarity : 0.004 0.038 2037 Dihedral : 9.860 85.075 1772 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.92 % Allowed : 19.27 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.31 (0.23), residues: 1430 helix: 2.40 (0.17), residues: 995 sheet: None (None), residues: 0 loop : -0.56 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 186 TYR 0.013 0.001 TYR A 408 PHE 0.012 0.001 PHE A 635 TRP 0.017 0.001 TRP A 338 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (12077) covalent geometry : angle 0.56927 / 0.27 (16522) hydrogen bonds : bond 0.03606 / 2.39 ( 785) hydrogen bonds : angle 4.07783 / 3.01 ( 2274) Misc. bond : bond 0.14421 / 7.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.9025 (tpp80) REVERT: A 494 GLU cc_start: 0.9052 (tt0) cc_final: 0.8561 (tm-30) REVERT: A 664 MET cc_start: 0.9728 (mmm) cc_final: 0.9515 (mmm) REVERT: B 67 MET cc_start: 0.8425 (mtt) cc_final: 0.8071 (mtt) REVERT: B 178 ASN cc_start: 0.9528 (OUTLIER) cc_final: 0.8762 (t0) REVERT: B 309 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6390 (mt-10) REVERT: B 583 MET cc_start: 0.9465 (mtm) cc_final: 0.9250 (mpp) REVERT: B 591 MET cc_start: 0.9530 (mtp) cc_final: 0.9015 (mtp) REVERT: B 664 MET cc_start: 0.9701 (mmm) cc_final: 0.9457 (mmm) outliers start: 33 outliers final: 13 residues processed: 115 average time/residue: 0.0870 time to fit residues: 15.5457 Evaluate side-chains 94 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 596 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [4, 83, 135, 16, 136, 82, 58, 138, 18, 114, 123] chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.059377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.051925 restraints weight = 50585.402| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.78 r_work: 0.2767 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.252 12081 Z= 0.130 Angle : 0.557 8.370 16522 Z= 0.259 Chirality : 0.038 0.250 1752 Planarity : 0.003 0.041 2037 Dihedral : 9.357 84.032 1759 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.98 % Allowed : 18.66 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.46 (0.24), residues: 1430 helix: 2.48 (0.17), residues: 1003 sheet: None (None), residues: 0 loop : -0.49 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 186 TYR 0.018 0.001 TYR B 638 PHE 0.011 0.001 PHE A 635 TRP 0.016 0.001 TRP A 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (12077) covalent geometry : angle 0.55710 / 0.26 (16522) hydrogen bonds : bond 0.03433 / 2.29 ( 785) hydrogen bonds : angle 4.00272 / 2.96 ( 2274) Misc. bond : bond 0.17632 / 8.87 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 ARG cc_start: 0.9372 (OUTLIER) cc_final: 0.8945 (mmm-85) REVERT: A 494 GLU cc_start: 0.9065 (tt0) cc_final: 0.8643 (tm-30) REVERT: A 579 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8080 (ptt-90) REVERT: A 591 MET cc_start: 0.9434 (mtp) cc_final: 0.9116 (mtp) REVERT: A 664 MET cc_start: 0.9717 (mmm) cc_final: 0.9465 (mmm) REVERT: B 67 MET cc_start: 0.8560 (mtt) cc_final: 0.8194 (mtt) REVERT: B 126 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.9075 (tm-30) REVERT: B 178 ASN cc_start: 0.9503 (OUTLIER) cc_final: 0.8869 (t0) REVERT: B 189 MET cc_start: 0.9740 (mmm) cc_final: 0.9519 (tpp) REVERT: B 309 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: B 591 MET cc_start: 0.9549 (mtp) cc_final: 0.9065 (mtp) outliers start: 45 outliers final: 20 residues processed: 118 average time/residue: 0.0902 time to fit residues: 16.3644 Evaluate side-chains 99 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [14, 113, 79, 50, 56, 128, 140, 91, 65, 119, 49] chunk 14 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.050466 restraints weight = 51894.315| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.83 r_work: 0.2732 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.343 12081 Z= 0.164 Angle : 0.586 10.861 16522 Z= 0.269 Chirality : 0.038 0.197 1752 Planarity : 0.003 0.042 2037 Dihedral : 9.283 83.616 1759 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.01 % Allowed : 19.81 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.55 (0.24), residues: 1430 helix: 2.58 (0.17), residues: 1005 sheet: None (None), residues: 0 loop : -0.54 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 703 TYR 0.014 0.001 TYR B 78 PHE 0.012 0.001 PHE A 635 TRP 0.017 0.001 TRP B 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.16 (12077) covalent geometry : angle 0.58646 / 0.27 (16522) hydrogen bonds : bond 0.03435 / 2.30 ( 785) hydrogen bonds : angle 3.98070 / 2.95 ( 2274) Misc. bond : bond 0.24874 / 12.48 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 432 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.8959 (mmm-85) REVERT: A 494 GLU cc_start: 0.9115 (tt0) cc_final: 0.8714 (tm-30) REVERT: A 579 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8111 (ptt-90) REVERT: A 664 MET cc_start: 0.9726 (mmm) cc_final: 0.9456 (mmm) REVERT: B 67 MET cc_start: 0.8664 (mtt) cc_final: 0.8291 (mtt) REVERT: B 126 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9114 (tm-30) REVERT: B 178 ASN cc_start: 0.9519 (OUTLIER) cc_final: 0.8954 (t0) REVERT: B 189 MET cc_start: 0.9765 (mmm) cc_final: 0.9435 (tpp) REVERT: B 309 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: B 494 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8536 (tm-30) REVERT: B 664 MET cc_start: 0.9717 (mmm) cc_final: 0.9501 (mmm) outliers start: 34 outliers final: 21 residues processed: 100 average time/residue: 0.0856 time to fit residues: 13.4385 Evaluate side-chains 95 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [55, 30, 27, 110, 72, 64, 41, 120, 43, 132, 93] chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 GLN B 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.049541 restraints weight = 52320.652| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.82 r_work: 0.2713 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.394 12081 Z= 0.185 Angle : 0.597 9.009 16522 Z= 0.275 Chirality : 0.038 0.203 1752 Planarity : 0.004 0.043 2037 Dihedral : 9.254 83.151 1759 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.45 % Allowed : 19.98 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.62 (0.24), residues: 1430 helix: 2.62 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -0.53 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 579 TYR 0.014 0.001 TYR B 78 PHE 0.013 0.001 PHE A 635 TRP 0.017 0.001 TRP B 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (12077) covalent geometry : angle 0.59671 / 0.27 (16522) hydrogen bonds : bond 0.03502 / 2.35 ( 785) hydrogen bonds : angle 3.99236 / 2.96 ( 2274) Misc. bond : bond 0.27934 / 13.99 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8713 (mtt) cc_final: 0.8362 (mtt) REVERT: A 432 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.8919 (mmm-85) REVERT: A 492 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: A 494 GLU cc_start: 0.9124 (tt0) cc_final: 0.8715 (tm-30) REVERT: A 579 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8125 (ptt-90) REVERT: A 591 MET cc_start: 0.9432 (mtm) cc_final: 0.9143 (mtp) REVERT: B 178 ASN cc_start: 0.9530 (OUTLIER) cc_final: 0.9034 (t0) REVERT: B 309 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: B 494 GLU cc_start: 0.9146 (tt0) cc_final: 0.8625 (tm-30) REVERT: B 591 MET cc_start: 0.9477 (mtm) cc_final: 0.9137 (mtp) outliers start: 39 outliers final: 26 residues processed: 101 average time/residue: 0.0843 time to fit residues: 13.5479 Evaluate side-chains 98 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [129, 134, 30, 97, 100, 102, 112, 21, 128, 61, 117] chunk 129 optimal weight: 0.1980 chunk 134 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 GLN B 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050063 restraints weight = 51841.169| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.83 r_work: 0.2733 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.315 12081 Z= 0.128 Angle : 0.571 8.234 16522 Z= 0.261 Chirality : 0.037 0.176 1752 Planarity : 0.003 0.042 2037 Dihedral : 9.125 83.422 1757 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.45 % Allowed : 19.98 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.60 (0.24), residues: 1430 helix: 2.58 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -0.47 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.016 0.001 TYR B 638 PHE 0.013 0.001 PHE B 635 TRP 0.016 0.001 TRP A 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (12077) covalent geometry : angle 0.57067 / 0.26 (16522) hydrogen bonds : bond 0.03370 / 2.26 ( 785) hydrogen bonds : angle 3.93375 / 2.92 ( 2274) Misc. bond : bond 0.21823 / 10.92 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 72 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8696 (mtt) cc_final: 0.8280 (mtt) REVERT: A 432 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.8944 (mmm-85) REVERT: A 494 GLU cc_start: 0.9116 (tt0) cc_final: 0.8698 (tm-30) REVERT: A 579 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8139 (ptt-90) REVERT: A 591 MET cc_start: 0.9405 (mtm) cc_final: 0.9117 (mtp) REVERT: B 178 ASN cc_start: 0.9531 (OUTLIER) cc_final: 0.9041 (t0) REVERT: B 189 MET cc_start: 0.9788 (OUTLIER) cc_final: 0.9496 (tpp) REVERT: B 309 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6519 (mt-10) REVERT: B 393 MET cc_start: 0.8693 (ttm) cc_final: 0.8410 (ttm) REVERT: B 494 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: B 591 MET cc_start: 0.9484 (mtp) cc_final: 0.9231 (mtp) outliers start: 39 outliers final: 28 residues processed: 101 average time/residue: 0.0836 time to fit residues: 13.4207 Evaluate side-chains 103 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 737 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [41, 53, 56, 102, 76, 80, 20, 93, 104, 4, 31] chunk 41 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 GLN B 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.049024 restraints weight = 52830.617| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.79 r_work: 0.2706 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.386 12081 Z= 0.192 Angle : 0.601 8.019 16522 Z= 0.280 Chirality : 0.038 0.236 1752 Planarity : 0.003 0.042 2037 Dihedral : 9.217 83.879 1757 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.45 % Allowed : 19.89 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.69 (0.24), residues: 1430 helix: 2.66 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -0.45 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.014 0.001 TYR B 78 PHE 0.013 0.001 PHE B 635 TRP 0.014 0.001 TRP B 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (12077) covalent geometry : angle 0.60084 / 0.28 (16522) hydrogen bonds : bond 0.03473 / 2.33 ( 785) hydrogen bonds : angle 3.98269 / 2.95 ( 2274) Misc. bond : bond 0.27552 / 13.81 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8697 (mtt) cc_final: 0.8323 (mtt) REVERT: A 432 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.8899 (mmm-85) REVERT: A 492 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: A 494 GLU cc_start: 0.9142 (tt0) cc_final: 0.8735 (tm-30) REVERT: A 579 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8149 (ptt-90) REVERT: A 591 MET cc_start: 0.9443 (mtp) cc_final: 0.9114 (mtp) REVERT: B 309 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6516 (mt-10) REVERT: B 393 MET cc_start: 0.8718 (ttm) cc_final: 0.8467 (ttm) REVERT: B 494 GLU cc_start: 0.9104 (tt0) cc_final: 0.8642 (tm-30) REVERT: B 591 MET cc_start: 0.9503 (mtp) cc_final: 0.9223 (mtp) outliers start: 39 outliers final: 31 residues processed: 99 average time/residue: 0.0777 time to fit residues: 12.2734 Evaluate side-chains 102 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 737 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [66, 13, 36, 117, 64, 120, 14, 12, 109, 17, 107] chunk 66 optimal weight: 3.9990 chunk 13 optimal weight: 0.0040 chunk 36 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.057422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.050091 restraints weight = 52271.040| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.82 r_work: 0.2742 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.277 12081 Z= 0.107 Angle : 0.565 9.087 16522 Z= 0.260 Chirality : 0.037 0.204 1752 Planarity : 0.003 0.042 2037 Dihedral : 9.014 83.792 1755 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.36 % Allowed : 20.07 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.60 (0.24), residues: 1430 helix: 2.59 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -0.48 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 186 TYR 0.013 0.001 TYR A 78 PHE 0.010 0.001 PHE A 635 TRP 0.018 0.001 TRP A 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.10 (12077) covalent geometry : angle 0.56520 / 0.26 (16522) hydrogen bonds : bond 0.03349 / 2.25 ( 785) hydrogen bonds : angle 3.90163 / 2.90 ( 2274) Misc. bond : bond 0.18946 / 9.47 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8662 (mtt) cc_final: 0.8235 (mtt) REVERT: A 393 MET cc_start: 0.8658 (ttm) cc_final: 0.8407 (ttm) REVERT: A 432 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.8884 (mmm-85) REVERT: A 492 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: A 494 GLU cc_start: 0.9097 (tt0) cc_final: 0.8697 (tm-30) REVERT: A 579 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8125 (ptt-90) REVERT: A 591 MET cc_start: 0.9402 (mtp) cc_final: 0.9087 (mtp) REVERT: B 126 GLU cc_start: 0.9532 (OUTLIER) cc_final: 0.9208 (tm-30) REVERT: B 189 MET cc_start: 0.9793 (OUTLIER) cc_final: 0.9303 (tpp) REVERT: B 309 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: B 393 MET cc_start: 0.8705 (ttm) cc_final: 0.8455 (ttm) REVERT: B 494 GLU cc_start: 0.9012 (tt0) cc_final: 0.8577 (tm-30) REVERT: B 591 MET cc_start: 0.9473 (mtp) cc_final: 0.9185 (mtp) outliers start: 38 outliers final: 29 residues processed: 104 average time/residue: 0.0840 time to fit residues: 13.7880 Evaluate side-chains 105 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [43, 109, 58, 75, 87, 37, 108, 85, 50, 77, 69] chunk 43 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 0.0670 chunk 77 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049613 restraints weight = 52298.110| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.80 r_work: 0.2728 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.299 12081 Z= 0.140 Angle : 0.578 8.296 16522 Z= 0.266 Chirality : 0.038 0.250 1752 Planarity : 0.003 0.042 2037 Dihedral : 9.044 84.123 1755 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.09 % Allowed : 20.60 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.68 (0.24), residues: 1430 helix: 2.64 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : -0.45 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.013 0.001 TYR A 78 PHE 0.011 0.001 PHE A 635 TRP 0.015 0.001 TRP A 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.14 (12077) covalent geometry : angle 0.57810 / 0.27 (16522) hydrogen bonds : bond 0.03319 / 2.23 ( 785) hydrogen bonds : angle 3.90372 / 2.89 ( 2274) Misc. bond : bond 0.21250 / 10.65 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8669 (mtt) cc_final: 0.8210 (mtt) REVERT: A 393 MET cc_start: 0.8718 (ttm) cc_final: 0.8475 (ttm) REVERT: A 432 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.8888 (mmm-85) REVERT: A 492 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: A 494 GLU cc_start: 0.9128 (tt0) cc_final: 0.8721 (tm-30) REVERT: A 579 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8124 (ptt-90) REVERT: A 591 MET cc_start: 0.9412 (mtp) cc_final: 0.9184 (mtp) REVERT: B 309 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: B 393 MET cc_start: 0.8712 (ttm) cc_final: 0.8470 (ttm) REVERT: B 494 GLU cc_start: 0.9068 (tt0) cc_final: 0.8630 (tm-30) outliers start: 35 outliers final: 29 residues processed: 97 average time/residue: 0.0831 time to fit residues: 12.9333 Evaluate side-chains 102 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [70, 7, 104, 62, 91, 43, 141, 75, 57, 10, 125] chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.048947 restraints weight = 51520.843| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.81 r_work: 0.2722 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.357 12081 Z= 0.180 Angle : 0.597 8.662 16522 Z= 0.277 Chirality : 0.039 0.229 1752 Planarity : 0.003 0.042 2037 Dihedral : 9.154 85.832 1755 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.01 % Allowed : 20.51 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.73 (0.24), residues: 1430 helix: 2.67 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : -0.42 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.015 0.001 TYR A 78 PHE 0.012 0.001 PHE A 635 TRP 0.014 0.001 TRP A 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (12077) covalent geometry : angle 0.59738 / 0.28 (16522) hydrogen bonds : bond 0.03435 / 2.31 ( 785) hydrogen bonds : angle 3.95157 / 2.93 ( 2274) Misc. bond : bond 0.25616 / 12.85 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8706 (mtt) cc_final: 0.8289 (mtt) REVERT: A 393 MET cc_start: 0.8748 (ttm) cc_final: 0.8515 (ttm) REVERT: A 432 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8884 (mmm-85) REVERT: A 492 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: A 494 GLU cc_start: 0.9150 (tt0) cc_final: 0.8736 (tm-30) REVERT: A 579 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8034 (ptt-90) REVERT: B 309 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: B 393 MET cc_start: 0.8732 (ttm) cc_final: 0.8490 (ttm) REVERT: B 494 GLU cc_start: 0.9072 (tt0) cc_final: 0.8657 (tm-30) REVERT: B 591 MET cc_start: 0.9431 (mtm) cc_final: 0.9182 (mtp) outliers start: 34 outliers final: 29 residues processed: 94 average time/residue: 0.0810 time to fit residues: 12.1162 Evaluate side-chains 101 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: [135, 69, 131, 98, 124, 2, 65, 129, 106, 72, 32] chunk 135 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.056519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.049576 restraints weight = 51194.722| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.65 r_work: 0.2739 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.314 12081 Z= 0.132 Angle : 0.589 11.444 16522 Z= 0.268 Chirality : 0.038 0.218 1752 Planarity : 0.003 0.042 2037 Dihedral : 9.060 84.681 1753 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.09 % Allowed : 20.69 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.69 (0.24), residues: 1430 helix: 2.62 (0.17), residues: 1013 sheet: None (None), residues: 0 loop : -0.38 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 717 TYR 0.015 0.001 TYR A 78 PHE 0.011 0.001 PHE A 635 TRP 0.016 0.001 TRP A 338 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.13 (12077) covalent geometry : angle 0.58878 / 0.27 (16522) hydrogen bonds : bond 0.03381 / 2.27 ( 785) hydrogen bonds : angle 3.89962 / 2.89 ( 2274) Misc. bond : bond 0.22056 / 11.05 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.08 seconds wall clock time: 42 minutes 7.45 seconds (2527.45 seconds total)