Starting phenix.real_space_refine on Fri Jul 3 07:09:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1g_39727/07_2026/8z1g_39727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1g_39727/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z1g_39727/07_2026/8z1g_39727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1g_39727/07_2026/8z1g_39727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z1g_39727/07_2026/8z1g_39727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1g_39727/07_2026/8z1g_39727.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.43, per 1000 atoms: 0.19 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: 1.13 Conformation dependent library (CDL) restraints added in 399.4 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: 2.58 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: 2.96 Time building geometry restraints manager: 1.60 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=" C ILE A 183 " pdb=" O ILE A 183 " ideal model delta sigma weight residual 1.232 1.241 -0.009 1.01e-02 9.80e+03 8.30e-01 bond pdb=" CA THR A 57 " pdb=" CB THR A 57 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.35e-02 5.49e+03 7.47e-01 ... (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=" 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 angle pdb=" C2' A T 66 " pdb=" C1' A T 66 " pdb=" H1' A T 66 " ideal model delta sigma weight residual 109.00 79.84 29.16 3.00e+00 1.11e-01 9.45e+01 angle pdb=" O4' A T 66 " pdb=" C1' A T 66 " pdb=" H1' A T 66 " ideal model delta sigma weight residual 109.00 80.38 28.62 3.00e+00 1.11e-01 9.10e+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 2.46 1.58 0.88 2.00e-01 2.50e+01 1.95e+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 2.46 1.58 0.88 2.00e-01 2.50e+01 1.92e+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: 4.780 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: 0.080 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.480 Find NCS groups from input model: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- 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= 0.111 Angle : 0.662 26.347 9999 Z= 0.365 Chirality : 0.075 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 0.00196 / 0.11 ( 7134) covalent geometry : angle 0.66183 / 0.37 ( 9999) hydrogen bonds : bond 0.19747 / 20.56 ( 221) hydrogen bonds : angle 6.66651 / 7.50 ( 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 : 0.331 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: 0.1843 time to fit residues: 20.1248 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 : 0.333 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 5.9990 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 = 0.4565 r_free = 0.4565 target = 0.200324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.154443 restraints weight = 32051.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162097 restraints weight = 15641.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.166812 restraints weight = 10188.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.169880 restraints weight = 7707.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.171838 restraints weight = 6371.849| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 7139 Z= 0.169 Angle : 0.694 26.740 9999 Z= 0.343 Chirality : 0.076 1.887 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.721 141.578 1789 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.72 % Favored : 93.99 % Rotamer: Outliers : 2.87 % Allowed : 17.57 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.35), residues: 682 helix: 2.02 (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 0.005 0.001 ARG A 251 TYR 0.008 0.001 TYR A 591 PHE 0.011 0.001 PHE A 85 TRP 0.005 0.001 TRP A 115 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 7134) covalent geometry : angle 0.69375 / 0.34 ( 9999) hydrogen bonds : bond 0.06022 / 6.21 ( 221) hydrogen bonds : angle 5.27472 / 6.15 ( 594) metal coordination : bond 0.00379 / 0.22 ( 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 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7531 (mmm) cc_final: 0.7284 (tpt) REVERT: A 264 LEU cc_start: 0.5001 (OUTLIER) cc_final: 0.4524 (mp) REVERT: A 289 ARG cc_start: 0.7660 (ptm160) cc_final: 0.7449 (ptm160) REVERT: A 358 MET cc_start: 0.7644 (ptt) cc_final: 0.7397 (ptt) REVERT: A 604 MET cc_start: 0.7276 (ptt) cc_final: 0.6936 (ptm) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.1296 time to fit residues: 15.5827 Evaluate side-chains 86 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 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: 0.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.196922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.150734 restraints weight = 31580.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.158266 restraints weight = 15538.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.162879 restraints weight = 10135.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.165876 restraints weight = 7699.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.167813 restraints weight = 6372.210| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7139 Z= 0.129 Angle : 0.658 26.706 9999 Z= 0.321 Chirality : 0.076 1.900 1181 Planarity : 0.004 0.042 1037 Dihedral : 18.792 140.565 1785 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.16 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: 0.84 (0.35), residues: 682 helix: 2.04 (0.38), residues: 211 sheet: 0.22 (0.51), residues: 126 loop : -0.20 (0.37), 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 0.010 0.001 PHE A 109 TRP 0.009 0.002 TRP A 115 HIS 0.004 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 7134) covalent geometry : angle 0.65782 / 0.32 ( 9999) hydrogen bonds : bond 0.05076 / 5.24 ( 221) hydrogen bonds : angle 4.70351 / 5.54 ( 594) metal coordination : bond 0.00237 / 0.15 ( 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 : 0.343 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: 0.7530 (mmm) cc_final: 0.7232 (tpt) REVERT: A 264 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4387 (mp) REVERT: A 358 MET cc_start: 0.7687 (ptt) cc_final: 0.7477 (ptt) REVERT: A 604 MET cc_start: 0.7388 (ptt) cc_final: 0.7019 (ptm) outliers start: 19 outliers final: 14 residues processed: 85 average time/residue: 0.1546 time to fit residues: 18.6722 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 : 0.307 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 426 GLN A 738 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.195253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.152707 restraints weight = 32042.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.158922 restraints weight = 17248.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.162919 restraints weight = 11830.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.165499 restraints weight = 9233.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.166920 restraints weight = 7789.861| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7139 Z= 0.231 Angle : 0.735 26.851 9999 Z= 0.371 Chirality : 0.077 1.915 1181 Planarity : 0.005 0.045 1037 Dihedral : 18.983 136.340 1785 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.62 % Favored : 92.08 % 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: 0.29 (0.34), residues: 682 helix: 1.75 (0.38), residues: 213 sheet: -0.55 (0.47), residues: 131 loop : -0.47 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.010 0.002 TYR A 663 PHE 0.019 0.002 PHE A 85 TRP 0.008 0.002 TRP A 115 HIS 0.007 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 ( 7134) covalent geometry : angle 0.73533 / 0.37 ( 9999) hydrogen bonds : bond 0.05093 / 5.17 ( 221) hydrogen bonds : angle 4.67256 / 5.57 ( 594) metal coordination : bond 0.00742 / 0.41 ( 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 95 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.344 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: 0.6723 (mm-30) cc_final: 0.6163 (pp20) REVERT: A 390 ASN cc_start: 0.7807 (t0) cc_final: 0.7505 (t0) REVERT: A 604 MET cc_start: 0.7354 (ptt) cc_final: 0.7010 (ptm) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.1341 time to fit residues: 16.3345 Evaluate side-chains 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP 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: 0.2980 chunk 2 optimal weight: 20.0000 chunk 43 optimal weight: 0.0980 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.198154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.155044 restraints weight = 31820.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.162124 restraints weight = 15555.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.166475 restraints weight = 10182.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.169198 restraints weight = 7763.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.170682 restraints weight = 6476.752| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7139 Z= 0.095 Angle : 0.652 26.517 9999 Z= 0.318 Chirality : 0.076 1.926 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.888 135.050 1779 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.72 % Favored : 93.99 % Rotamer: Outliers : 3.38 % Allowed : 17.40 % 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: 0.60 (0.35), residues: 682 helix: 2.02 (0.38), residues: 214 sheet: -0.47 (0.49), residues: 126 loop : -0.24 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.006 0.001 TYR A 463 PHE 0.008 0.001 PHE A 521 TRP 0.013 0.001 TRP A 115 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 7134) covalent geometry : angle 0.65161 / 0.32 ( 9999) hydrogen bonds : bond 0.03865 / 3.91 ( 221) hydrogen bonds : angle 4.40890 / 5.21 ( 594) metal coordination : bond 0.00131 / 0.08 ( 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 97 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.274 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: 0.7526 (mmm) cc_final: 0.7201 (tpt) REVERT: A 130 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6007 (pp20) REVERT: A 264 LEU cc_start: 0.5075 (OUTLIER) cc_final: 0.4488 (mp) REVERT: A 604 MET cc_start: 0.7416 (ptt) cc_final: 0.7027 (ptm) outliers start: 20 outliers final: 18 residues processed: 88 average time/residue: 0.1378 time to fit residues: 17.0499 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 : 0.339 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.196703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.153536 restraints weight = 31528.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.160486 restraints weight = 15592.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.164848 restraints weight = 10301.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.167193 restraints weight = 7865.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.169148 restraints weight = 6670.519| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7139 Z= 0.123 Angle : 0.653 26.640 9999 Z= 0.318 Chirality : 0.076 1.923 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.887 133.780 1779 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.04 % Favored : 92.67 % Rotamer: Outliers : 3.38 % Allowed : 17.91 % 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: 0.65 (0.35), residues: 682 helix: 2.11 (0.38), residues: 214 sheet: -0.52 (0.49), residues: 126 loop : -0.22 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 526 TYR 0.007 0.001 TYR A 463 PHE 0.010 0.001 PHE A 521 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 0.00277 / 0.12 ( 7134) covalent geometry : angle 0.65328 / 0.32 ( 9999) hydrogen bonds : bond 0.03763 / 3.82 ( 221) hydrogen bonds : angle 4.35903 / 5.12 ( 594) metal coordination : bond 0.00302 / 0.18 ( 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 94 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.202 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: 0.6606 (mm-30) cc_final: 0.6025 (pp20) REVERT: A 264 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4492 (mp) REVERT: A 358 MET cc_start: 0.8092 (ptm) cc_final: 0.7555 (ptt) REVERT: A 604 MET cc_start: 0.7410 (ptt) cc_final: 0.7018 (ptm) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.1349 time to fit residues: 16.3073 Evaluate side-chains 89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.193584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.152968 restraints weight = 31755.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.157996 restraints weight = 18809.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.161313 restraints weight = 12780.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.161871 restraints weight = 10643.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.162044 restraints weight = 9774.499| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7139 Z= 0.187 Angle : 0.704 26.579 9999 Z= 0.352 Chirality : 0.077 1.934 1181 Planarity : 0.005 0.050 1037 Dihedral : 19.029 129.823 1779 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.92 % Favored : 91.79 % Rotamer: Outliers : 4.22 % Allowed : 17.57 % Favored : 78.21 % 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: 0.23 (0.35), residues: 682 helix: 1.81 (0.37), residues: 214 sheet: -0.87 (0.47), residues: 131 loop : -0.45 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 781 TYR 0.010 0.001 TYR A 663 PHE 0.022 0.002 PHE A 254 TRP 0.007 0.002 TRP A 357 HIS 0.007 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 7134) covalent geometry : angle 0.70386 / 0.35 ( 9999) hydrogen bonds : bond 0.04183 / 4.25 ( 221) hydrogen bonds : angle 4.46002 / 5.32 ( 594) metal coordination : bond 0.00786 / 0.43 ( 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 97 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.326 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: 0.6624 (mm-30) cc_final: 0.6032 (pp20) REVERT: A 264 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4597 (mp) REVERT: A 358 MET cc_start: 0.8211 (ptm) cc_final: 0.7607 (ptt) REVERT: A 550 ASP cc_start: 0.7973 (p0) cc_final: 0.7729 (p0) REVERT: A 778 MET cc_start: 0.5278 (ptm) cc_final: 0.5074 (ptm) REVERT: A 782 ARG cc_start: 0.6258 (mmt180) cc_final: 0.6035 (mmt180) outliers start: 25 outliers final: 19 residues processed: 88 average time/residue: 0.1465 time to fit residues: 18.0827 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 : 0.200 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 4 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4553 r_free = 0.4553 target = 0.195618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.152176 restraints weight = 31623.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.159211 restraints weight = 15872.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.163496 restraints weight = 10451.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.166223 restraints weight = 8039.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.167728 restraints weight = 6744.044| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2677 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= 0.097 Angle : 0.657 26.382 9999 Z= 0.321 Chirality : 0.076 1.940 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.971 129.159 1779 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.01 % Favored : 93.70 % Rotamer: Outliers : 3.38 % Allowed : 18.41 % Favored : 78.21 % 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: 0.51 (0.35), residues: 682 helix: 2.07 (0.38), residues: 213 sheet: -0.77 (0.49), residues: 126 loop : -0.28 (0.38), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.007 0.001 TYR A 463 PHE 0.009 0.001 PHE A 109 TRP 0.010 0.001 TRP A 115 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 7134) covalent geometry : angle 0.65670 / 0.32 ( 9999) hydrogen bonds : bond 0.03559 / 3.60 ( 221) hydrogen bonds : angle 4.28840 / 5.03 ( 594) metal coordination : bond 0.00200 / 0.12 ( 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 94 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.251 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: 0.7614 (mmm) cc_final: 0.7263 (tpt) REVERT: A 130 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6113 (pp20) REVERT: A 264 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4456 (mp) REVERT: A 358 MET cc_start: 0.8163 (ptm) cc_final: 0.7577 (ptt) REVERT: A 417 VAL cc_start: 0.7549 (OUTLIER) cc_final: 0.7306 (m) REVERT: A 550 ASP cc_start: 0.7793 (p0) cc_final: 0.7578 (p0) outliers start: 20 outliers final: 16 residues processed: 86 average time/residue: 0.1284 time to fit residues: 15.7390 Evaluate side-chains 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 644 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.194515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.150824 restraints weight = 31851.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.157855 restraints weight = 16010.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.162148 restraints weight = 10602.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.164818 restraints weight = 8164.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.166327 restraints weight = 6863.325| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7139 Z= 0.125 Angle : 0.667 26.462 9999 Z= 0.326 Chirality : 0.076 1.937 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.967 128.309 1779 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.48 % Favored : 92.23 % Rotamer: Outliers : 2.87 % Allowed : 18.75 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.35), residues: 682 helix: 2.04 (0.38), residues: 214 sheet: -0.90 (0.47), residues: 131 loop : -0.27 (0.38), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 782 TYR 0.007 0.001 TYR A 463 PHE 0.010 0.001 PHE A 254 TRP 0.006 0.001 TRP A 115 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7134) covalent geometry : angle 0.66673 / 0.33 ( 9999) hydrogen bonds : bond 0.03580 / 3.66 ( 221) hydrogen bonds : angle 4.27796 / 5.00 ( 594) metal coordination : bond 0.00364 / 0.20 ( 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 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.328 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 130 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6125 (pp20) REVERT: A 358 MET cc_start: 0.8198 (ptm) cc_final: 0.7633 (ptt) REVERT: A 417 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7335 (m) REVERT: A 550 ASP cc_start: 0.7832 (p0) cc_final: 0.7608 (p0) outliers start: 17 outliers final: 16 residues processed: 82 average time/residue: 0.1401 time to fit residues: 16.0225 Evaluate side-chains 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 3 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.192189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.151137 restraints weight = 32002.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.157848 restraints weight = 19831.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.159960 restraints weight = 12249.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.160547 restraints weight = 10269.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.161105 restraints weight = 10089.658| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3118 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= 0.157 Angle : 0.692 26.385 9999 Z= 0.345 Chirality : 0.077 1.947 1181 Planarity : 0.007 0.130 1037 Dihedral : 19.067 125.557 1779 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.36 % Favored : 91.35 % Rotamer: Outliers : 2.70 % Allowed : 19.26 % 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: 0.12 (0.35), residues: 682 helix: 1.78 (0.37), residues: 216 sheet: -1.14 (0.47), residues: 133 loop : -0.47 (0.38), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 782 TYR 0.010 0.001 TYR A 663 PHE 0.016 0.002 PHE A 109 TRP 0.006 0.002 TRP A 357 HIS 0.008 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7134) covalent geometry : angle 0.69156 / 0.35 ( 9999) hydrogen bonds : bond 0.03911 / 4.06 ( 221) hydrogen bonds : angle 4.38548 / 5.14 ( 594) metal coordination : bond 0.00814 / 0.43 ( 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 89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.328 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 130 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6116 (pp20) REVERT: A 358 MET cc_start: 0.8252 (ptm) cc_final: 0.7719 (ptt) REVERT: A 417 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7410 (m) REVERT: A 550 ASP cc_start: 0.7924 (p0) cc_final: 0.7722 (p0) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.1480 time to fit residues: 16.8835 Evaluate side-chains 86 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 713 MET Chi-restraints excluded: chain A residue 716 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4525 r_free = 0.4525 target = 0.193134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.148415 restraints weight = 31607.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.155468 restraints weight = 16000.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.159687 restraints weight = 10670.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.162387 restraints weight = 8296.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.163856 restraints weight = 7018.780| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7139 Z= 0.118 Angle : 0.682 26.345 9999 Z= 0.338 Chirality : 0.077 1.948 1181 Planarity : 0.005 0.050 1037 Dihedral : 19.022 125.859 1779 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.92 % Favored : 91.79 % Rotamer: Outliers : 2.53 % Allowed : 19.93 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.35), residues: 682 helix: 1.90 (0.37), residues: 215 sheet: -1.10 (0.47), residues: 132 loop : -0.46 (0.38), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 782 TYR 0.007 0.001 TYR A 463 PHE 0.009 0.001 PHE A 109 TRP 0.007 0.001 TRP A 115 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7134) covalent geometry : angle 0.68199 / 0.34 ( 9999) hydrogen bonds : bond 0.03716 / 3.87 ( 221) hydrogen bonds : angle 4.36529 / 5.08 ( 594) metal coordination : bond 0.00337 / 0.19 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.86 seconds wall clock time: 43 minutes 37.79 seconds (2617.79 seconds total)