Starting phenix.real_space_refine on Thu Aug 6 01:25:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1g_39727/08_2026/8z1g_39727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1g_39727/08_2026/8z1g_39727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1g_39727/08_2026/8z1g_39727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1g_39727/08_2026/8z1g_39727.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1g_39727/08_2026/8z1g_39727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1g_39727/08_2026/8z1g_39727.cif" } resolution = 3.7 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= 0.007 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 69 5.49 5 S 38 5.16 5 C 4066 2.51 5 N 1207 2.21 5 O 1463 1.98 5 H 6138 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12983 Number of models: 1 Model: "" Number of chains: 3 Chain: "T" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 2187 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 23} Link IDs: {'rna2p': 14, 'rna3p': 53} Chain: "A" Number of atoms: 10789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 10789 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 41, 'TRANS': 646} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.73, per 1000 atoms: 0.13 Number of scatterers: 12983 At special positions: 0 Unit cell: (68.38, 94.154, 128.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 69 15.00 O 1463 8.00 N 1207 7.00 C 4066 6.00 H 6138 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: 1.21 Conformation dependent library (CDL) restraints added in 417.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 548 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 546 " pdb="ZN ZN A 901 " - pdb="ZN ZN A 902 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 551 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 724 " 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1292 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 7 sheets defined 39.2% alpha, 14.2% beta 15 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.669A pdb=" N TYR A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.848A pdb=" N MET A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.886A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.502A pdb=" N GLU A 295 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.933A pdb=" N ARG A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 379 through 391 removed outlier: 3.618A pdb=" N HIS A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.660A pdb=" N PHE A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.764A pdb=" N HIS A 552 " --> pdb=" O HIS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 Processing helix chain 'A' and resid 581 through 591 removed outlier: 3.931A pdb=" N LYS A 585 " --> pdb=" O PRO A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 693 through 701 Processing helix chain 'A' and resid 704 through 716 removed outlier: 3.585A pdb=" N ASN A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.612A pdb=" N ALA A 730 " --> pdb=" O GLN A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 757 removed outlier: 3.548A pdb=" N PHE A 757 " --> pdb=" O PHE A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 762 removed outlier: 3.897A pdb=" N LYS A 762 " --> pdb=" O THR A 759 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 759 through 762' Processing helix chain 'A' and resid 763 through 771 Processing helix chain 'A' and resid 772 through 793 removed outlier: 4.018A pdb=" N GLU A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.573A pdb=" N ALA A 73 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 424 " --> pdb=" O GLN A 434 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 432 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.074A pdb=" N ILE A 108 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 180 removed outlier: 7.352A pdb=" N ALA A 305 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 340 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 307 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS A 342 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 309 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 417 " --> pdb=" O HIS A 367 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 369 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.650A pdb=" N ALA A 242 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.980A pdb=" N ALA A 540 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL A 579 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 542 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER A 511 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 542 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 506 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 503 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 485 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A 505 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 483 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A 750 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 634 through 641 removed outlier: 4.914A pdb=" N VAL A 654 " --> pdb=" O GLU A 635 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE A 637 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 652 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR A 639 " --> pdb=" O GLY A 650 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 650 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS A 660 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE A 684 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 662 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 683 " --> pdb=" O MET A 721 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.71 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: 6118 1.03 - 1.23: 98 1.23 - 1.43: 3087 1.43 - 1.62: 3913 1.62 - 1.82: 56 Bond restraints: 13272 Sorted by residual: bond pdb=" N SER A 52 " pdb=" CA SER A 52 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N SER A 52 " pdb=" H SER A 52 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" N9 A T 38 " pdb=" C4 A T 38 " ideal model delta sigma weight residual 1.374 1.381 -0.007 6.00e-03 2.78e+04 1.53e+00 bond pdb=" C4' A T 32 " pdb=" C3' A T 32 " ideal model delta sigma weight residual 1.521 1.533 -0.012 1.00e-02 1.00e+04 1.44e+00 bond pdb=" C4' A T 66 " pdb=" C3' A T 66 " ideal model delta sigma weight residual 1.521 1.533 -0.012 1.00e-02 1.00e+04 1.41e+00 ... (remaining 13267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.74: 23992 6.74 - 13.47: 6 13.47 - 20.21: 0 20.21 - 26.94: 2 26.94 - 33.68: 6 Bond angle restraints: 24006 Sorted by residual: angle pdb=" O4' A T 66 " pdb=" C1' A T 66 " pdb=" N9 A T 66 " ideal model delta sigma weight residual 108.50 117.49 -8.99 7.00e-01 2.04e+00 1.65e+02 angle pdb=" O4' A T 32 " pdb=" C1' A T 32 " pdb=" N9 A T 32 " ideal model delta sigma weight residual 108.50 117.28 -8.78 7.00e-01 2.04e+00 1.57e+02 angle pdb=" N9 A T 32 " pdb=" C1' A T 32 " pdb=" H1' A T 32 " ideal model delta sigma weight residual 109.00 75.32 33.68 3.00e+00 1.11e-01 1.26e+02 angle pdb=" N9 A T 66 " pdb=" C1' A T 66 " pdb=" H1' A T 66 " ideal model delta sigma weight residual 109.00 75.65 33.35 3.00e+00 1.11e-01 1.24e+02 angle pdb=" C2' A T 32 " pdb=" C1' A T 32 " pdb=" H1' A T 32 " ideal model delta sigma weight residual 109.00 79.78 29.22 3.00e+00 1.11e-01 9.49e+01 ... (remaining 24001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 5872 28.56 - 57.11: 343 57.11 - 85.67: 110 85.67 - 114.23: 4 114.23 - 142.78: 1 Dihedral angle restraints: 6330 sinusoidal: 4024 harmonic: 2306 Sorted by residual: dihedral pdb=" O4' U T 60 " pdb=" C1' U T 60 " pdb=" N1 U T 60 " pdb=" C2 U T 60 " ideal model delta sinusoidal sigma weight residual -160.00 -17.22 -142.78 1 1.50e+01 4.44e-03 7.66e+01 dihedral pdb=" O4' U T 37 " pdb=" C1' U T 37 " pdb=" N1 U T 37 " pdb=" C2 U T 37 " ideal model delta sinusoidal sigma weight residual 200.00 86.82 113.18 1 1.50e+01 4.44e-03 5.95e+01 dihedral pdb=" O4' C T 36 " pdb=" C1' C T 36 " pdb=" N1 C T 36 " pdb=" C2 C T 36 " ideal model delta sinusoidal sigma weight residual -160.00 -76.44 -83.56 1 1.50e+01 4.44e-03 3.79e+01 ... (remaining 6327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 1178 0.381 - 0.762: 0 0.762 - 1.142: 2 1.142 - 1.523: 0 1.523 - 1.904: 1 Chirality restraints: 1181 Sorted by residual: chirality pdb=" P A T 66 " pdb=" OP1 A T 66 " pdb=" OP2 A T 66 " pdb=" O5' A T 66 " both_signs ideal model delta sigma weight residual True 2.41 0.51 1.90 2.00e-01 2.50e+01 9.06e+01 chirality pdb=" C1' A T 66 " pdb=" O4' A T 66 " pdb=" C2' A T 66 " pdb=" N9 A T 66 " both_signs ideal model delta sigma weight residual False 2.47 1.58 0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" C1' A T 32 " pdb=" O4' A T 32 " pdb=" C2' A T 32 " pdb=" N9 A T 32 " both_signs ideal model delta sigma weight residual False 2.47 1.58 0.89 2.00e-01 2.50e+01 1.98e+01 ... (remaining 1178 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 623 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ARG A 623 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG A 623 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 624 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 251 " 0.160 9.50e-02 1.11e+02 5.35e-02 3.13e+00 pdb=" NE ARG A 251 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 251 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 251 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 251 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 251 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 251 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 251 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 251 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 764 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.72e+00 pdb=" N PRO A 765 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 765 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 765 " 0.023 5.00e-02 4.00e+02 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 400 2.15 - 2.76: 22519 2.76 - 3.37: 34606 3.37 - 3.99: 43210 3.99 - 4.60: 67486 Nonbonded interactions: 168221 Sorted by model distance: nonbonded pdb=" O TYR A 591 " pdb=" HD1 HIS A 592 " model vdw 1.534 2.450 nonbonded pdb=" O6 G T 9 " pdb=" H62 A T 19 " model vdw 1.643 2.450 nonbonded pdb="HD21 ASN A 390 " pdb=" O PHE A 397 " model vdw 1.646 2.450 nonbonded pdb=" H ILE A 720 " pdb=" O LYS A 742 " model vdw 1.651 2.450 nonbonded pdb=" OE1 GLU A 145 " pdb=" H GLU A 145 " model vdw 1.656 2.450 ... (remaining 168216 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 group one per residue 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: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 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 0.033 7139 Z= 0.121 Angle : 0.717 26.347 9999 Z= 0.475 Chirality : 0.079 1.904 1181 Planarity : 0.004 0.070 1037 Dihedral : 19.188 142.782 3101 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.96 % Favored : 95.75 % Rotamer: Outliers : 1.01 % Allowed : 18.24 % Favored : 80.74 % 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: 1.26 (0.35), residues: 682 helix: 2.27 (0.39), residues: 210 sheet: 0.93 (0.53), residues: 128 loop : -0.07 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.005 0.000 TYR A 528 PHE 0.006 0.000 PHE A 521 TRP 0.002 0.000 TRP A 115 HIS 0.003 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.12 ( 7134) covalent geometry : angle 0.71697 / 0.48 ( 9999) hydrogen bonds : bond 0.19747 / 21.86 ( 221) hydrogen bonds : angle 6.66651 / 7.78 ( 594) metal coordination : bond 0.00038 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.330 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: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7361 (mmm) cc_final: 0.7097 (tpt) REVERT: A 264 LEU cc_start: 0.5044 (OUTLIER) cc_final: 0.4667 (mt) REVERT: A 289 ARG cc_start: 0.7506 (ptm160) cc_final: 0.7281 (ptm160) REVERT: A 358 MET cc_start: 0.7516 (ptt) cc_final: 0.7234 (ptt) REVERT: A 604 MET cc_start: 0.7297 (ptt) cc_final: 0.6972 (ptm) outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 0.1673 time to fit residues: 18.3578 Evaluate side-chains 75 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 775 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.200744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.154881 restraints weight = 31662.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.162601 restraints weight = 15388.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.167381 restraints weight = 9961.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.170467 restraints weight = 7511.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.172151 restraints weight = 6191.846| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7139 Z= 0.167 Angle : 0.689 27.017 9999 Z= 0.336 Chirality : 0.069 1.832 1181 Planarity : 0.004 0.044 1037 Dihedral : 18.674 140.886 1789 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.72 % Favored : 93.99 % Rotamer: Outliers : 2.87 % Allowed : 17.23 % Favored : 79.90 % 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: 0.95 (0.35), residues: 682 helix: 2.01 (0.38), residues: 211 sheet: 0.57 (0.50), residues: 130 loop : -0.18 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 251 TYR 0.009 0.001 TYR A 591 PHE 0.013 0.001 PHE A 85 TRP 0.006 0.001 TRP A 115 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 7134) covalent geometry : angle 0.68922 / 0.34 ( 9999) hydrogen bonds : bond 0.06133 / 6.76 ( 221) hydrogen bonds : angle 5.27386 / 6.49 ( 594) metal coordination : bond 0.00383 / 0.25 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.309 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 124 MET cc_start: 0.7539 (mmm) cc_final: 0.7297 (tpt) REVERT: A 264 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4530 (mp) REVERT: A 289 ARG cc_start: 0.7660 (ptm160) cc_final: 0.7449 (ptm160) REVERT: A 358 MET cc_start: 0.7643 (ptt) cc_final: 0.7369 (ptt) REVERT: A 604 MET cc_start: 0.7283 (ptt) cc_final: 0.6941 (ptm) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.1430 time to fit residues: 17.2376 Evaluate side-chains 87 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.197036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150237 restraints weight = 31535.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.157817 restraints weight = 15533.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.162464 restraints weight = 10166.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.165451 restraints weight = 7726.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.167174 restraints weight = 6423.671| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7139 Z= 0.129 Angle : 0.644 26.429 9999 Z= 0.314 Chirality : 0.068 1.891 1181 Planarity : 0.004 0.042 1037 Dihedral : 18.757 140.295 1785 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.28 % Favored : 94.43 % Rotamer: Outliers : 3.21 % Allowed : 17.57 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.35), residues: 682 helix: 2.02 (0.38), residues: 211 sheet: 0.23 (0.51), residues: 126 loop : -0.21 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.007 0.001 TYR A 663 PHE 0.011 0.001 PHE A 109 TRP 0.010 0.002 TRP A 115 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7134) covalent geometry : angle 0.64390 / 0.31 ( 9999) hydrogen bonds : bond 0.05031 / 5.53 ( 221) hydrogen bonds : angle 4.72926 / 5.86 ( 594) metal coordination : bond 0.00255 / 0.19 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.361 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: symmetry clash REVERT: A 124 MET cc_start: 0.7532 (mmm) cc_final: 0.7239 (tpt) REVERT: A 264 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4384 (mp) REVERT: A 358 MET cc_start: 0.7694 (ptt) cc_final: 0.7481 (ptt) REVERT: A 604 MET cc_start: 0.7361 (ptt) cc_final: 0.6994 (ptm) outliers start: 19 outliers final: 14 residues processed: 85 average time/residue: 0.1534 time to fit residues: 18.3972 Evaluate side-chains 88 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.196579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.153000 restraints weight = 31946.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.159977 restraints weight = 16024.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.164216 restraints weight = 10617.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166965 restraints weight = 8166.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168460 restraints weight = 6841.071| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7139 Z= 0.191 Angle : 0.702 26.633 9999 Z= 0.345 Chirality : 0.069 1.871 1181 Planarity : 0.005 0.044 1037 Dihedral : 18.929 136.357 1785 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.04 % Favored : 92.67 % Rotamer: Outliers : 3.38 % Allowed : 17.74 % Favored : 78.89 % 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: 0.47 (0.34), residues: 682 helix: 1.91 (0.38), residues: 213 sheet: -0.42 (0.49), residues: 126 loop : -0.38 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.008 0.001 TYR A 463 PHE 0.016 0.002 PHE A 521 TRP 0.006 0.002 TRP A 115 HIS 0.006 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 7134) covalent geometry : angle 0.70227 / 0.35 ( 9999) hydrogen bonds : bond 0.04849 / 5.27 ( 221) hydrogen bonds : angle 4.55556 / 5.74 ( 594) metal coordination : bond 0.00548 / 0.32 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.270 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: symmetry clash REVERT: A 130 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6021 (pp20) REVERT: A 604 MET cc_start: 0.7385 (ptt) cc_final: 0.7018 (ptm) outliers start: 20 outliers final: 16 residues processed: 87 average time/residue: 0.1360 time to fit residues: 16.7988 Evaluate side-chains 89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.196345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.152972 restraints weight = 31986.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.159982 restraints weight = 15783.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.164271 restraints weight = 10402.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166957 restraints weight = 7968.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.168444 restraints weight = 6663.757| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7139 Z= 0.142 Angle : 0.654 26.252 9999 Z= 0.321 Chirality : 0.069 1.895 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.926 134.141 1779 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.45 % Favored : 93.26 % Rotamer: Outliers : 3.55 % Allowed : 17.40 % Favored : 79.05 % 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: 0.46 (0.35), residues: 682 helix: 1.92 (0.37), residues: 214 sheet: -0.58 (0.49), residues: 126 loop : -0.33 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.008 0.001 TYR A 663 PHE 0.012 0.002 PHE A 109 TRP 0.011 0.002 TRP A 115 HIS 0.008 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7134) covalent geometry : angle 0.65407 / 0.32 ( 9999) hydrogen bonds : bond 0.04058 / 4.41 ( 221) hydrogen bonds : angle 4.47153 / 5.63 ( 594) metal coordination : bond 0.00310 / 0.28 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.325 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: symmetry clash REVERT: A 130 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6042 (pp20) REVERT: A 264 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4501 (mp) REVERT: A 604 MET cc_start: 0.7449 (ptt) cc_final: 0.7055 (ptm) outliers start: 21 outliers final: 19 residues processed: 84 average time/residue: 0.1431 time to fit residues: 17.1199 Evaluate side-chains 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 716 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.197994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.157559 restraints weight = 31546.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.164047 restraints weight = 19439.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.167130 restraints weight = 12237.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.167409 restraints weight = 9439.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.167550 restraints weight = 9405.695| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 7139 Z= 0.094 Angle : 0.629 26.127 9999 Z= 0.303 Chirality : 0.068 1.897 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.876 133.561 1779 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.45 % Favored : 93.26 % Rotamer: Outliers : 3.21 % Allowed : 18.07 % Favored : 78.72 % 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: 0.62 (0.35), residues: 682 helix: 2.09 (0.38), residues: 214 sheet: -0.55 (0.49), residues: 126 loop : -0.24 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 782 TYR 0.006 0.001 TYR A 463 PHE 0.028 0.001 PHE A 316 TRP 0.011 0.001 TRP A 115 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 ( 7134) covalent geometry : angle 0.62934 / 0.30 ( 9999) hydrogen bonds : bond 0.03629 / 3.94 ( 221) hydrogen bonds : angle 4.32523 / 5.42 ( 594) metal coordination : bond 0.00136 / 0.13 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.299 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: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7529 (mmm) cc_final: 0.7182 (tpt) REVERT: A 130 GLU cc_start: 0.6568 (mm-30) cc_final: 0.5969 (pp20) REVERT: A 358 MET cc_start: 0.8058 (ptm) cc_final: 0.7514 (ptt) REVERT: A 604 MET cc_start: 0.7430 (ptt) cc_final: 0.7032 (ptm) outliers start: 19 outliers final: 18 residues processed: 84 average time/residue: 0.1287 time to fit residues: 15.3293 Evaluate side-chains 88 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 775 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.195108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.151766 restraints weight = 31704.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.158643 restraints weight = 15898.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.162948 restraints weight = 10558.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.165324 restraints weight = 8090.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.167227 restraints weight = 6867.460| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7139 Z= 0.152 Angle : 0.659 26.175 9999 Z= 0.320 Chirality : 0.068 1.891 1181 Planarity : 0.004 0.046 1037 Dihedral : 18.940 131.188 1779 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.62 % Favored : 92.08 % Rotamer: Outliers : 3.89 % Allowed : 18.24 % Favored : 77.87 % 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: 0.45 (0.35), residues: 682 helix: 2.01 (0.38), residues: 214 sheet: -0.74 (0.49), residues: 126 loop : -0.34 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 781 TYR 0.008 0.001 TYR A 663 PHE 0.014 0.002 PHE A 85 TRP 0.011 0.002 TRP A 115 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 7134) covalent geometry : angle 0.65869 / 0.32 ( 9999) hydrogen bonds : bond 0.03827 / 4.16 ( 221) hydrogen bonds : angle 4.34841 / 5.50 ( 594) metal coordination : bond 0.00651 / 0.41 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.198 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: symmetry clash REVERT: A 130 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6097 (pp20) REVERT: A 264 LEU cc_start: 0.5102 (OUTLIER) cc_final: 0.4504 (mp) REVERT: A 358 MET cc_start: 0.8162 (ptm) cc_final: 0.7590 (ptt) REVERT: A 604 MET cc_start: 0.7426 (ptt) cc_final: 0.7026 (ptm) REVERT: A 778 MET cc_start: 0.5546 (ptm) cc_final: 0.5318 (ptm) outliers start: 23 outliers final: 19 residues processed: 84 average time/residue: 0.1179 time to fit residues: 14.0879 Evaluate side-chains 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 775 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.195931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.155244 restraints weight = 31703.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.161280 restraints weight = 19246.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.163934 restraints weight = 12443.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.164363 restraints weight = 10269.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.164681 restraints weight = 9771.538| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7139 Z= 0.106 Angle : 0.631 25.951 9999 Z= 0.304 Chirality : 0.068 1.900 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.939 129.875 1779 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.30 % Favored : 93.40 % Rotamer: Outliers : 3.55 % Allowed : 18.41 % Favored : 78.04 % 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: 0.56 (0.35), residues: 682 helix: 2.09 (0.38), residues: 214 sheet: -0.76 (0.49), residues: 126 loop : -0.23 (0.38), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 562 TYR 0.007 0.001 TYR A 463 PHE 0.009 0.001 PHE A 109 TRP 0.005 0.001 TRP A 115 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7134) covalent geometry : angle 0.63146 / 0.30 ( 9999) hydrogen bonds : bond 0.03451 / 3.76 ( 221) hydrogen bonds : angle 4.25903 / 5.34 ( 594) metal coordination : bond 0.00208 / 0.22 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.305 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: symmetry clash REVERT: A 130 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6011 (pp20) REVERT: A 264 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4548 (mp) REVERT: A 358 MET cc_start: 0.8155 (ptm) cc_final: 0.7632 (ptt) REVERT: A 417 VAL cc_start: 0.7607 (OUTLIER) cc_final: 0.7363 (m) outliers start: 21 outliers final: 18 residues processed: 87 average time/residue: 0.1383 time to fit residues: 17.1190 Evaluate side-chains 93 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 775 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4544 r_free = 0.4544 target = 0.194531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149931 restraints weight = 31643.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156968 restraints weight = 15845.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.161217 restraints weight = 10524.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.163907 restraints weight = 8149.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.165424 restraints weight = 6882.434| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7139 Z= 0.134 Angle : 0.647 25.970 9999 Z= 0.314 Chirality : 0.069 1.897 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.957 128.972 1779 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.48 % Favored : 92.23 % Rotamer: Outliers : 3.38 % Allowed : 18.07 % Favored : 78.55 % 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: 0.47 (0.35), residues: 682 helix: 2.05 (0.38), residues: 214 sheet: -0.83 (0.49), residues: 126 loop : -0.29 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.008 0.001 TYR A 663 PHE 0.014 0.001 PHE A 254 TRP 0.006 0.001 TRP A 115 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7134) covalent geometry : angle 0.64731 / 0.31 ( 9999) hydrogen bonds : bond 0.03556 / 3.88 ( 221) hydrogen bonds : angle 4.26947 / 5.35 ( 594) metal coordination : bond 0.00372 / 0.27 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.311 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: symmetry clash REVERT: A 130 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6110 (pp20) REVERT: A 358 MET cc_start: 0.8204 (ptm) cc_final: 0.7673 (ptt) REVERT: A 417 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7342 (m) REVERT: A 550 ASP cc_start: 0.7835 (p0) cc_final: 0.7609 (p0) REVERT: A 778 MET cc_start: 0.5467 (ptm) cc_final: 0.5262 (ptm) outliers start: 20 outliers final: 19 residues processed: 83 average time/residue: 0.1394 time to fit residues: 16.3299 Evaluate side-chains 91 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 775 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 6 optimal weight: 0.0070 chunk 67 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 22 optimal weight: 0.0570 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.196277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.155724 restraints weight = 31972.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.161638 restraints weight = 19174.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.163233 restraints weight = 12449.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.163810 restraints weight = 11050.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.164080 restraints weight = 10280.515| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7139 Z= 0.091 Angle : 0.628 25.776 9999 Z= 0.300 Chirality : 0.068 1.900 1181 Planarity : 0.004 0.050 1037 Dihedral : 18.901 128.687 1779 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.16 % Favored : 93.55 % Rotamer: Outliers : 3.21 % Allowed : 18.24 % Favored : 78.55 % 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: 0.65 (0.36), residues: 682 helix: 2.23 (0.38), residues: 213 sheet: -0.74 (0.49), residues: 126 loop : -0.20 (0.38), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 526 TYR 0.005 0.001 TYR A 463 PHE 0.009 0.001 PHE A 243 TRP 0.009 0.001 TRP A 115 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 7134) covalent geometry : angle 0.62815 / 0.30 ( 9999) hydrogen bonds : bond 0.03222 / 3.54 ( 221) hydrogen bonds : angle 4.15319 / 5.18 ( 594) metal coordination : bond 0.00109 / 0.10 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.355 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7556 (mmm) cc_final: 0.7193 (tpt) REVERT: A 130 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6003 (pp20) REVERT: A 358 MET cc_start: 0.8164 (ptm) cc_final: 0.7736 (ptt) REVERT: A 417 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7341 (m) outliers start: 19 outliers final: 17 residues processed: 85 average time/residue: 0.1473 time to fit residues: 17.8158 Evaluate side-chains 91 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 574 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 775 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 0.0000 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.196104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.152813 restraints weight = 31734.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.159813 restraints weight = 15846.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.164115 restraints weight = 10497.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.166736 restraints weight = 8052.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.168147 restraints weight = 6778.038| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7139 Z= 0.099 Angle : 0.640 25.792 9999 Z= 0.307 Chirality : 0.069 1.895 1181 Planarity : 0.004 0.046 1037 Dihedral : 18.867 128.553 1779 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.89 % Favored : 92.82 % Rotamer: Outliers : 3.04 % Allowed : 18.92 % Favored : 78.04 % 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: 0.58 (0.35), residues: 682 helix: 2.16 (0.37), residues: 214 sheet: -0.70 (0.49), residues: 125 loop : -0.27 (0.38), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.005 0.001 TYR A 463 PHE 0.008 0.001 PHE A 254 TRP 0.008 0.001 TRP A 115 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 7134) covalent geometry : angle 0.64045 / 0.31 ( 9999) hydrogen bonds : bond 0.03223 / 3.56 ( 221) hydrogen bonds : angle 4.21564 / 5.17 ( 594) metal coordination : bond 0.00148 / 0.12 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.11 seconds wall clock time: 42 minutes 52.36 seconds (2572.36 seconds total)