Starting phenix.real_space_refine on Wed Jul 30 21:13:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1g_39727/07_2025/8z1g_39727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1g_39727/07_2025/8z1g_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_39727/07_2025/8z1g_39727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1g_39727/07_2025/8z1g_39727.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1g_39727/07_2025/8z1g_39727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1g_39727/07_2025/8z1g_39727.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.02, per 1000 atoms: 0.62 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: 3.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 6.09 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: 5.50 Time building geometry restraints manager: 4.28 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=" 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 bond pdb=" C MET A 760 " pdb=" N PRO A 761 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.69e-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: 46.090 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: 0.180 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 42.570 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 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= 0.101 Angle : 0.662 26.347 9999 Z= 0.324 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 : 5.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (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 TRP 0.002 0.000 TRP A 115 HIS 0.003 0.000 HIS A 114 PHE 0.006 0.000 PHE A 521 TYR 0.005 0.000 TYR A 528 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.19747 ( 221) hydrogen bonds : angle 6.66651 ( 594) metal coordination : bond 0.00038 ( 5) covalent geometry : bond 0.00196 ( 7134) covalent geometry : angle 0.66179 ( 9999) *********************** 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 : 0.970 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: 0.4314 time to fit residues: 46.9881 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 : 0.949 ------------------------------------------------------------------------------- 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 62 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN A 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.194676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.147373 restraints weight = 31697.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.154715 restraints weight = 16016.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159320 restraints weight = 10690.333| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7139 Z= 0.211 Angle : 0.760 26.944 9999 Z= 0.375 Chirality : 0.077 1.877 1181 Planarity : 0.005 0.053 1037 Dihedral : 18.857 140.172 1789 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.87 % Favored : 93.84 % Rotamer: Outliers : 3.04 % Allowed : 16.55 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.34), residues: 682 helix: 1.71 (0.37), residues: 211 sheet: 0.12 (0.50), residues: 128 loop : -0.30 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 115 HIS 0.007 0.002 HIS A 114 PHE 0.024 0.002 PHE A 85 TYR 0.012 0.002 TYR A 663 ARG 0.008 0.001 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.05726 ( 221) hydrogen bonds : angle 4.94416 ( 594) metal coordination : bond 0.00688 ( 5) covalent geometry : bond 0.00473 ( 7134) covalent geometry : angle 0.76039 ( 9999) *********************** 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 93 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.006 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 264 LEU cc_start: 0.4964 (OUTLIER) cc_final: 0.4383 (mp) REVERT: A 289 ARG cc_start: 0.7691 (ptm160) cc_final: 0.7450 (ptm160) REVERT: A 604 MET cc_start: 0.7428 (ptt) cc_final: 0.7053 (ptm) outliers start: 18 outliers final: 13 residues processed: 85 average time/residue: 0.4168 time to fit residues: 49.6625 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 : 0.981 ------------------------------------------------------------------------------- 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 538 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN 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 = 0.195248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.148109 restraints weight = 31461.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.155669 restraints weight = 15530.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.160399 restraints weight = 10185.350| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1599 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= 0.112 Angle : 0.666 26.657 9999 Z= 0.318 Chirality : 0.075 1.914 1181 Planarity : 0.004 0.042 1037 Dihedral : 18.794 139.064 1785 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.28 % Favored : 94.43 % Rotamer: Outliers : 3.21 % Allowed : 17.06 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.35), residues: 682 helix: 1.98 (0.38), residues: 212 sheet: 0.01 (0.50), residues: 128 loop : -0.22 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.004 0.001 HIS A 551 PHE 0.009 0.001 PHE A 109 TYR 0.006 0.001 TYR A 147 ARG 0.002 0.000 ARG A 781 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 221) hydrogen bonds : angle 4.58018 ( 594) metal coordination : bond 0.00189 ( 5) covalent geometry : bond 0.00245 ( 7134) covalent geometry : angle 0.66597 ( 9999) *********************** 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 96 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.456 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: 0.7437 (mmm) cc_final: 0.7116 (tpt) REVERT: A 130 GLU cc_start: 0.6223 (mm-30) cc_final: 0.5525 (pp20) REVERT: A 264 LEU cc_start: 0.4987 (OUTLIER) cc_final: 0.4405 (mp) REVERT: A 604 MET cc_start: 0.7438 (ptt) cc_final: 0.7040 (ptm) outliers start: 19 outliers final: 14 residues processed: 87 average time/residue: 0.5215 time to fit residues: 63.8907 Evaluate side-chains 89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 428 ARG Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 539 LEU 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 738 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.197492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.153329 restraints weight = 31445.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.160371 restraints weight = 15520.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164654 restraints weight = 10296.754| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7139 Z= 0.144 Angle : 0.678 26.748 9999 Z= 0.326 Chirality : 0.076 1.911 1181 Planarity : 0.004 0.046 1037 Dihedral : 18.849 136.717 1785 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.01 % Favored : 93.70 % Rotamer: Outliers : 3.04 % Allowed : 17.57 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.35), residues: 682 helix: 1.99 (0.38), residues: 213 sheet: -0.27 (0.49), residues: 126 loop : -0.23 (0.37), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 115 HIS 0.004 0.001 HIS A 114 PHE 0.011 0.001 PHE A 85 TYR 0.007 0.001 TYR A 663 ARG 0.002 0.000 ARG A 782 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 221) hydrogen bonds : angle 4.44078 ( 594) metal coordination : bond 0.00361 ( 5) covalent geometry : bond 0.00323 ( 7134) covalent geometry : angle 0.67773 ( 9999) *********************** 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: 18 poor density : 77 time to evaluate : 1.548 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 130 GLU cc_start: 0.6257 (mm-30) cc_final: 0.5732 (pp20) REVERT: A 604 MET cc_start: 0.7403 (ptt) cc_final: 0.7016 (ptm) outliers start: 18 outliers final: 17 residues processed: 86 average time/residue: 0.5054 time to fit residues: 62.8959 Evaluate side-chains 92 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 428 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.197185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.154018 restraints weight = 31796.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.161079 restraints weight = 15617.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.165393 restraints weight = 10260.212| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7139 Z= 0.118 Angle : 0.664 26.615 9999 Z= 0.318 Chirality : 0.076 1.925 1181 Planarity : 0.004 0.044 1037 Dihedral : 18.860 133.758 1783 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.16 % Favored : 93.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.35), residues: 682 helix: 2.15 (0.38), residues: 212 sheet: -0.44 (0.49), residues: 126 loop : -0.20 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 115 HIS 0.004 0.001 HIS A 114 PHE 0.010 0.001 PHE A 109 TYR 0.006 0.001 TYR A 463 ARG 0.002 0.000 ARG A 104 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 221) hydrogen bonds : angle 4.29809 ( 594) metal coordination : bond 0.00180 ( 5) covalent geometry : bond 0.00263 ( 7134) covalent geometry : angle 0.66370 ( 9999) *********************** 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 93 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 2.009 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 130 GLU cc_start: 0.6321 (mm-30) cc_final: 0.5890 (pp20) REVERT: A 358 MET cc_start: 0.8090 (ptm) cc_final: 0.7555 (ptt) REVERT: A 604 MET cc_start: 0.7431 (ptt) cc_final: 0.7034 (ptm) outliers start: 19 outliers final: 18 residues processed: 84 average time/residue: 0.4361 time to fit residues: 53.1903 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 : 1.057 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.192752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.148859 restraints weight = 32297.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.155826 restraints weight = 16018.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.160158 restraints weight = 10631.807| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7139 Z= 0.169 Angle : 0.700 26.530 9999 Z= 0.341 Chirality : 0.077 1.932 1181 Planarity : 0.005 0.045 1037 Dihedral : 18.976 128.652 1779 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.92 % Favored : 91.79 % Rotamer: Outliers : 4.22 % Allowed : 17.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.35), residues: 682 helix: 1.89 (0.38), residues: 214 sheet: -0.80 (0.47), residues: 131 loop : -0.27 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 115 HIS 0.006 0.001 HIS A 114 PHE 0.016 0.002 PHE A 85 TYR 0.010 0.001 TYR A 663 ARG 0.002 0.000 ARG A 104 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 221) hydrogen bonds : angle 4.35806 ( 594) metal coordination : bond 0.00630 ( 5) covalent geometry : bond 0.00379 ( 7134) covalent geometry : angle 0.70012 ( 9999) *********************** 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 97 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.885 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 130 GLU cc_start: 0.6254 (mm-30) cc_final: 0.5852 (pp20) REVERT: A 264 LEU cc_start: 0.5096 (OUTLIER) cc_final: 0.4488 (mp) REVERT: A 358 MET cc_start: 0.8236 (ptm) cc_final: 0.7664 (ptt) REVERT: A 715 MET cc_start: 0.5098 (tpt) cc_final: 0.4733 (tpt) outliers start: 25 outliers final: 21 residues processed: 88 average time/residue: 0.3759 time to fit residues: 46.1629 Evaluate side-chains 94 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 92 GLN 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 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 738 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.194358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.149717 restraints weight = 31805.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156897 restraints weight = 15755.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.161220 restraints weight = 10397.799| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2800 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= 0.104 Angle : 0.664 26.449 9999 Z= 0.318 Chirality : 0.076 1.941 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.922 127.719 1779 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.45 % Favored : 93.26 % Rotamer: Outliers : 2.70 % Allowed : 18.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.35), residues: 682 helix: 2.07 (0.38), residues: 215 sheet: -0.79 (0.49), residues: 126 loop : -0.19 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 115 HIS 0.004 0.001 HIS A 114 PHE 0.009 0.001 PHE A 109 TYR 0.007 0.001 TYR A 463 ARG 0.002 0.000 ARG A 104 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 221) hydrogen bonds : angle 4.19303 ( 594) metal coordination : bond 0.00174 ( 5) covalent geometry : bond 0.00236 ( 7134) covalent geometry : angle 0.66376 ( 9999) *********************** 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 89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.843 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 130 GLU cc_start: 0.6181 (mm-30) cc_final: 0.5888 (pp20) REVERT: A 358 MET cc_start: 0.8237 (ptm) cc_final: 0.7680 (ptt) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.3435 time to fit residues: 38.6698 Evaluate side-chains 87 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.192535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148104 restraints weight = 31954.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.155183 restraints weight = 15923.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.159468 restraints weight = 10584.345| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3021 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= 0.154 Angle : 0.688 26.409 9999 Z= 0.333 Chirality : 0.077 1.940 1181 Planarity : 0.004 0.045 1037 Dihedral : 18.957 125.943 1779 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.48 % Favored : 92.23 % Rotamer: Outliers : 3.55 % Allowed : 17.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.35), residues: 682 helix: 1.86 (0.37), residues: 216 sheet: -0.97 (0.47), residues: 131 loop : -0.22 (0.38), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 115 HIS 0.006 0.001 HIS A 114 PHE 0.013 0.001 PHE A 85 TYR 0.009 0.001 TYR A 663 ARG 0.002 0.000 ARG A 104 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 221) hydrogen bonds : angle 4.28678 ( 594) metal coordination : bond 0.00594 ( 5) covalent geometry : bond 0.00347 ( 7134) covalent geometry : angle 0.68765 ( 9999) *********************** 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: 21 poor density : 73 time to evaluate : 0.863 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 130 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5858 (pp20) REVERT: A 358 MET cc_start: 0.8301 (ptm) cc_final: 0.7750 (ptt) outliers start: 21 outliers final: 17 residues processed: 86 average time/residue: 0.3578 time to fit residues: 42.9131 Evaluate side-chains 89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.0470 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.195600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.151105 restraints weight = 31549.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.158261 restraints weight = 15687.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.162635 restraints weight = 10428.169| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3001 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 : 0.666 26.350 9999 Z= 0.317 Chirality : 0.077 1.943 1181 Planarity : 0.004 0.046 1037 Dihedral : 18.860 126.740 1779 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.57 % Favored : 94.13 % Rotamer: Outliers : 2.53 % Allowed : 18.07 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.36), residues: 682 helix: 2.07 (0.37), residues: 215 sheet: -0.83 (0.48), residues: 127 loop : -0.18 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 115 HIS 0.003 0.001 HIS A 114 PHE 0.010 0.001 PHE A 243 TYR 0.005 0.001 TYR A 173 ARG 0.002 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 221) hydrogen bonds : angle 4.17328 ( 594) metal coordination : bond 0.00070 ( 5) covalent geometry : bond 0.00207 ( 7134) covalent geometry : angle 0.66617 ( 9999) *********************** 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 87 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.001 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: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5890 (pp20) REVERT: A 358 MET cc_start: 0.8249 (ptm) cc_final: 0.7829 (ptt) outliers start: 15 outliers final: 15 residues processed: 81 average time/residue: 0.4112 time to fit residues: 45.3049 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 : 0.944 ------------------------------------------------------------------------------- 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 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 72 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.193581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.149016 restraints weight = 31651.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.155912 restraints weight = 15812.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.160251 restraints weight = 10609.805| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3123 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= 0.122 Angle : 0.672 26.352 9999 Z= 0.322 Chirality : 0.076 1.937 1181 Planarity : 0.004 0.046 1037 Dihedral : 18.861 125.540 1779 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.48 % Favored : 92.23 % Rotamer: Outliers : 2.87 % Allowed : 18.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.35), residues: 682 helix: 2.02 (0.37), residues: 216 sheet: -0.97 (0.47), residues: 132 loop : -0.17 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 115 HIS 0.005 0.001 HIS A 114 PHE 0.010 0.001 PHE A 109 TYR 0.008 0.001 TYR A 663 ARG 0.002 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 221) hydrogen bonds : angle 4.19831 ( 594) metal coordination : bond 0.00502 ( 5) covalent geometry : bond 0.00276 ( 7134) covalent geometry : angle 0.67154 ( 9999) ********************** 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 86 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.852 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 130 GLU cc_start: 0.6149 (mm-30) cc_final: 0.5894 (pp20) REVERT: A 358 MET cc_start: 0.8274 (ptm) cc_final: 0.7865 (ptt) outliers start: 17 outliers final: 17 residues processed: 79 average time/residue: 0.3869 time to fit residues: 41.4219 Evaluate side-chains 86 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.194382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.151074 restraints weight = 31448.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.158181 restraints weight = 15408.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.162564 restraints weight = 10094.412| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7139 Z= 0.101 Angle : 0.672 26.315 9999 Z= 0.320 Chirality : 0.076 1.939 1181 Planarity : 0.004 0.046 1037 Dihedral : 18.822 125.683 1779 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.16 % Favored : 93.55 % Rotamer: Outliers : 2.87 % Allowed : 18.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.35), residues: 682 helix: 2.01 (0.37), residues: 217 sheet: -0.91 (0.48), residues: 127 loop : -0.16 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.004 0.001 HIS A 114 PHE 0.007 0.001 PHE A 521 TYR 0.005 0.001 TYR A 463 ARG 0.006 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 221) hydrogen bonds : angle 3.99445 ( 594) metal coordination : bond 0.00192 ( 5) covalent geometry : bond 0.00233 ( 7134) covalent geometry : angle 0.67181 ( 9999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6597.00 seconds wall clock time: 119 minutes 57.16 seconds (7197.16 seconds total)