Starting phenix.real_space_refine on Tue Aug 4 22:18:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izm_61037/08_2026/9izm_61037.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izm_61037/08_2026/9izm_61037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izm_61037/08_2026/9izm_61037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izm_61037/08_2026/9izm_61037.map" model { file = "/net/cci-nas-00/data/ceres_data/9izm_61037/08_2026/9izm_61037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izm_61037/08_2026/9izm_61037.cif" } resolution = 3.02 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 ------------------------------------------------------------------------------- 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= 0.016 sd= 0.217 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 4388 2.51 5 N 1192 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7160 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6137 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 12, 'TRANS': 726} Chain: "B" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1021 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 16} Link IDs: {'rna2p': 11, 'rna3p': 36} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.19, per 1000 atoms: 0.17 Number of scatterers: 7160 At special positions: 0 Unit cell: (94.62, 98.355, 100.845, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 48 15.00 Mg 2 11.99 O 1500 8.00 N 1192 7.00 C 4388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 309.7 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 53.5% alpha, 8.8% beta 9 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 removed outlier: 3.655A pdb=" N ILE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.514A pdb=" N MET A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.664A pdb=" N LEU A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 149 through 165 removed outlier: 3.544A pdb=" N GLN A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.509A pdb=" N PHE A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 4.091A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.618A pdb=" N ASN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.566A pdb=" N ASP A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 removed outlier: 3.973A pdb=" N HIS A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.800A pdb=" N THR A 359 " --> pdb=" O HIS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.538A pdb=" N LYS A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 420 through 458 Processing helix chain 'A' and resid 467 through 478 removed outlier: 3.633A pdb=" N LYS A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 519 Processing helix chain 'A' and resid 541 through 547 removed outlier: 3.556A pdb=" N LEU A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 removed outlier: 4.234A pdb=" N ASN A 553 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A 554 " --> pdb=" O LEU A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 554' Processing helix chain 'A' and resid 562 through 571 removed outlier: 3.558A pdb=" N LYS A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 605 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 678 through 693 removed outlier: 3.615A pdb=" N VAL A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 720 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.587A pdb=" N ILE A 5 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER A 305 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN A 290 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.828A pdb=" N LYS A 242 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 258 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379 removed outlier: 5.614A pdb=" N VAL A 377 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY A 322 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LYS A 337 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 12.927A pdb=" N THR A 320 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 321 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLU A 526 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LEU A 323 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 578 Processing sheet with id=AA6, first strand: chain 'A' and resid 658 through 660 Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702 291 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1487 1.33 - 1.45: 1863 1.45 - 1.57: 3901 1.57 - 1.69: 95 1.69 - 1.81: 47 Bond restraints: 7393 Sorted by residual: bond pdb=" C2 G B -13 " pdb=" N3 G B -13 " ideal model delta sigma weight residual 1.323 1.306 0.017 8.00e-03 1.56e+04 4.63e+00 bond pdb=" C2 U B -29 " pdb=" N3 U B -29 " ideal model delta sigma weight residual 1.373 1.358 0.015 7.00e-03 2.04e+04 4.51e+00 bond pdb=" C5 G B -30 " pdb=" C4 G B -30 " ideal model delta sigma weight residual 1.379 1.366 0.013 7.00e-03 2.04e+04 3.31e+00 bond pdb=" N3 C B -1 " pdb=" C4 C B -1 " ideal model delta sigma weight residual 1.335 1.322 0.013 7.00e-03 2.04e+04 3.30e+00 bond pdb=" C6 A B -3 " pdb=" N1 A B -3 " ideal model delta sigma weight residual 1.351 1.340 0.011 7.00e-03 2.04e+04 2.56e+00 ... (remaining 7388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 9659 1.37 - 2.73: 456 2.73 - 4.10: 52 4.10 - 5.46: 3 5.46 - 6.83: 4 Bond angle restraints: 10174 Sorted by residual: angle pdb=" N GLU A 212 " pdb=" CA GLU A 212 " pdb=" C GLU A 212 " ideal model delta sigma weight residual 112.93 106.82 6.11 1.33e+00 5.65e-01 2.11e+01 angle pdb=" O5' U B -18 " pdb=" C5' U B -18 " pdb=" C4' U B -18 " ideal model delta sigma weight residual 109.40 112.55 -3.15 8.00e-01 1.56e+00 1.55e+01 angle pdb=" O5' A B -16 " pdb=" C5' A B -16 " pdb=" C4' A B -16 " ideal model delta sigma weight residual 109.40 112.52 -3.12 8.00e-01 1.56e+00 1.53e+01 angle pdb=" O5' A B -28 " pdb=" C5' A B -28 " pdb=" C4' A B -28 " ideal model delta sigma weight residual 109.40 112.38 -2.98 8.00e-01 1.56e+00 1.39e+01 angle pdb=" O5' A B -6 " pdb=" C5' A B -6 " pdb=" C4' A B -6 " ideal model delta sigma weight residual 109.40 112.08 -2.68 8.00e-01 1.56e+00 1.12e+01 ... (remaining 10169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.76: 4058 18.76 - 37.52: 356 37.52 - 56.27: 81 56.27 - 75.03: 61 75.03 - 93.79: 7 Dihedral angle restraints: 4563 sinusoidal: 2353 harmonic: 2210 Sorted by residual: dihedral pdb=" O4' U B 5 " pdb=" C1' U B 5 " pdb=" N1 U B 5 " pdb=" C2 U B 5 " ideal model delta sinusoidal sigma weight residual -128.00 -71.32 -56.68 1 1.70e+01 3.46e-03 1.50e+01 dihedral pdb=" O4' U B -22 " pdb=" C1' U B -22 " pdb=" N1 U B -22 " pdb=" C2 U B -22 " ideal model delta sinusoidal sigma weight residual -128.00 -72.23 -55.77 1 1.70e+01 3.46e-03 1.45e+01 dihedral pdb=" CA GLU A 445 " pdb=" C GLU A 445 " pdb=" N LYS A 446 " pdb=" CA LYS A 446 " ideal model delta harmonic sigma weight residual 180.00 162.39 17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 4560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 621 0.030 - 0.059: 333 0.059 - 0.088: 107 0.088 - 0.118: 49 0.118 - 0.147: 40 Chirality restraints: 1150 Sorted by residual: chirality pdb=" C1' A B 2 " pdb=" O4' A B 2 " pdb=" C2' A B 2 " pdb=" N9 A B 2 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA VAL A 633 " pdb=" N VAL A 633 " pdb=" C VAL A 633 " pdb=" CB VAL A 633 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" C2' A B -5 " pdb=" C3' A B -5 " pdb=" O2' A B -5 " pdb=" C1' A B -5 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1147 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 637 " -0.011 2.00e-02 2.50e+03 1.31e-02 2.99e+00 pdb=" CG PHE A 637 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 637 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 637 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 637 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 637 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 637 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 72 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 73 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B -24 " -0.020 2.00e-02 2.50e+03 8.88e-03 2.17e+00 pdb=" N9 A B -24 " 0.019 2.00e-02 2.50e+03 pdb=" C8 A B -24 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B -24 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A B -24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B -24 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B -24 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B -24 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B -24 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B -24 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B -24 " 0.004 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 48 2.50 - 3.10: 5129 3.10 - 3.70: 10950 3.70 - 4.30: 17265 4.30 - 4.90: 26356 Nonbonded interactions: 59748 Sorted by model distance: nonbonded pdb=" OP1 G B -30 " pdb="MG MG B 102 " model vdw 1.902 2.170 nonbonded pdb=" O2' C B -1 " pdb=" OP1 G B 1 " model vdw 2.124 3.040 nonbonded pdb=" OE2 GLU A 401 " pdb=" OG SER A 405 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR A 349 " pdb=" OE2 GLU A 383 " model vdw 2.207 3.040 nonbonded pdb=" NZ LYS A 24 " pdb=" OD1 ASN A 232 " model vdw 2.209 3.120 ... (remaining 59743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.005 0.048 7393 Z= 0.261 Angle : 0.659 6.828 10174 Z= 0.451 Chirality : 0.047 0.147 1150 Planarity : 0.004 0.045 1116 Dihedral : 16.450 93.788 3135 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.87 % Allowed : 7.56 % Favored : 91.57 % 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: -0.79 (0.30), residues: 737 helix: 0.31 (0.27), residues: 356 sheet: -1.26 (0.58), residues: 73 loop : -1.25 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 197 TYR 0.019 0.002 TYR A 23 PHE 0.030 0.002 PHE A 637 TRP 0.008 0.002 TRP A 69 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.26 ( 7393) covalent geometry : angle 0.65875 / 0.45 (10174) hydrogen bonds : bond 0.18302 / 11.85 ( 311) hydrogen bonds : angle 6.59418 / 4.63 ( 883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 PHE cc_start: 0.7883 (m-80) cc_final: 0.7617 (m-10) REVERT: A 155 MET cc_start: 0.6982 (mmm) cc_final: 0.6568 (mmm) REVERT: A 206 MET cc_start: 0.7119 (tpp) cc_final: 0.6813 (tpp) REVERT: A 227 MET cc_start: 0.8410 (ttm) cc_final: 0.8006 (ttm) REVERT: A 391 TYR cc_start: 0.8139 (t80) cc_final: 0.7846 (t80) REVERT: A 545 LEU cc_start: 0.7728 (tp) cc_final: 0.7489 (tp) REVERT: A 589 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: A 614 SER cc_start: 0.8619 (m) cc_final: 0.8377 (t) REVERT: A 640 GLN cc_start: 0.7380 (tt0) cc_final: 0.7052 (tm-30) REVERT: A 708 GLU cc_start: 0.7015 (tt0) cc_final: 0.6722 (tt0) outliers start: 6 outliers final: 0 residues processed: 186 average time/residue: 0.0740 time to fit residues: 18.0984 Evaluate side-chains 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 ASN A 230 HIS A 255 ASN A 297 ASN A 402 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.197995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.158003 restraints weight = 9034.049| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.90 r_work: 0.3686 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 7393 Z= 0.158 Angle : 0.588 6.598 10174 Z= 0.329 Chirality : 0.041 0.183 1150 Planarity : 0.004 0.031 1116 Dihedral : 17.545 92.484 1532 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.18 % Allowed : 13.08 % Favored : 84.74 % 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: -0.73 (0.30), residues: 737 helix: 0.40 (0.26), residues: 370 sheet: -1.28 (0.57), residues: 71 loop : -1.34 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.018 0.002 TYR A 92 PHE 0.021 0.002 PHE A 637 TRP 0.009 0.002 TRP A 69 HIS 0.012 0.002 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 7393) covalent geometry : angle 0.58846 / 0.33 (10174) hydrogen bonds : bond 0.05604 / 3.61 ( 311) hydrogen bonds : angle 4.99897 / 3.48 ( 883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 197 ARG cc_start: 0.6768 (mtm-85) cc_final: 0.6544 (mtm-85) REVERT: A 206 MET cc_start: 0.7364 (tpp) cc_final: 0.7112 (tpp) REVERT: A 211 LEU cc_start: 0.7167 (mt) cc_final: 0.6954 (mt) REVERT: A 212 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6529 (mp0) REVERT: A 227 MET cc_start: 0.8395 (ttm) cc_final: 0.8025 (ttm) REVERT: A 391 TYR cc_start: 0.8002 (t80) cc_final: 0.7564 (t80) REVERT: A 399 LYS cc_start: 0.8205 (tptt) cc_final: 0.7993 (tppt) REVERT: A 589 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: A 606 MET cc_start: 0.8882 (mtm) cc_final: 0.8657 (mtm) REVERT: A 609 SER cc_start: 0.8608 (t) cc_final: 0.8178 (t) REVERT: A 614 SER cc_start: 0.8685 (m) cc_final: 0.8381 (t) REVERT: A 708 GLU cc_start: 0.6965 (tt0) cc_final: 0.6599 (tt0) outliers start: 15 outliers final: 6 residues processed: 137 average time/residue: 0.0746 time to fit residues: 13.3296 Evaluate side-chains 117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 487 ASN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.194680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.155459 restraints weight = 8990.435| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.13 r_work: 0.3617 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 7393 Z= 0.239 Angle : 0.608 6.418 10174 Z= 0.334 Chirality : 0.043 0.170 1150 Planarity : 0.004 0.048 1116 Dihedral : 17.535 92.168 1532 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.05 % Allowed : 13.37 % Favored : 83.58 % 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: -0.97 (0.30), residues: 737 helix: 0.24 (0.26), residues: 376 sheet: -1.58 (0.57), residues: 75 loop : -1.47 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 192 TYR 0.023 0.003 TYR A 75 PHE 0.024 0.002 PHE A 478 TRP 0.010 0.002 TRP A 268 HIS 0.003 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 ( 7393) covalent geometry : angle 0.60760 / 0.33 (10174) hydrogen bonds : bond 0.05511 / 3.53 ( 311) hydrogen bonds : angle 4.90115 / 3.44 ( 883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6924 (tm-30) REVERT: A 212 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6536 (mp0) REVERT: A 218 GLN cc_start: 0.7861 (tt0) cc_final: 0.7657 (tm-30) REVERT: A 589 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: A 609 SER cc_start: 0.8609 (t) cc_final: 0.8173 (t) REVERT: A 614 SER cc_start: 0.8799 (m) cc_final: 0.8473 (t) REVERT: A 640 GLN cc_start: 0.7961 (tt0) cc_final: 0.7186 (tm-30) REVERT: A 651 LYS cc_start: 0.8376 (pttt) cc_final: 0.8060 (pttm) REVERT: A 708 GLU cc_start: 0.7066 (tt0) cc_final: 0.6693 (tt0) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 0.0761 time to fit residues: 12.3708 Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 0.0270 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 554 GLN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.195306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153726 restraints weight = 9095.965| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.16 r_work: 0.3638 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.005 0.082 7393 Z= 0.206 Angle : 0.571 7.256 10174 Z= 0.313 Chirality : 0.041 0.165 1150 Planarity : 0.004 0.038 1116 Dihedral : 17.479 92.222 1532 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.20 % Allowed : 13.81 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.30), residues: 737 helix: 0.37 (0.26), residues: 377 sheet: -1.69 (0.56), residues: 73 loop : -1.51 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 474 TYR 0.023 0.002 TYR A 75 PHE 0.015 0.002 PHE A 121 TRP 0.014 0.002 TRP A 33 HIS 0.007 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 7393) covalent geometry : angle 0.57123 / 0.31 (10174) hydrogen bonds : bond 0.05047 / 3.21 ( 311) hydrogen bonds : angle 4.79054 / 3.35 ( 883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7532 (ttm) cc_final: 0.7202 (ttm) REVERT: A 48 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7729 (mmtm) REVERT: A 52 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6755 (tm-30) REVERT: A 155 MET cc_start: 0.7687 (mmm) cc_final: 0.7486 (mmm) REVERT: A 212 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6564 (mp0) REVERT: A 588 LYS cc_start: 0.7454 (ttpp) cc_final: 0.7219 (ttpp) REVERT: A 589 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6153 (m-80) REVERT: A 609 SER cc_start: 0.8606 (t) cc_final: 0.8162 (t) REVERT: A 614 SER cc_start: 0.8745 (m) cc_final: 0.8461 (t) REVERT: A 640 GLN cc_start: 0.8014 (tt0) cc_final: 0.7141 (tm-30) REVERT: A 708 GLU cc_start: 0.7098 (tt0) cc_final: 0.6701 (tt0) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.0676 time to fit residues: 11.1980 Evaluate side-chains 114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 498 GLN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.194047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.154312 restraints weight = 9062.919| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.17 r_work: 0.3615 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 7393 Z= 0.240 Angle : 0.584 6.181 10174 Z= 0.320 Chirality : 0.042 0.163 1150 Planarity : 0.004 0.047 1116 Dihedral : 17.489 91.883 1532 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.05 % Allowed : 14.24 % Favored : 82.70 % 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: -0.90 (0.30), residues: 737 helix: 0.41 (0.26), residues: 377 sheet: -1.70 (0.57), residues: 73 loop : -1.59 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.024 0.003 TYR A 75 PHE 0.017 0.002 PHE A 637 TRP 0.014 0.002 TRP A 33 HIS 0.006 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 ( 7393) covalent geometry : angle 0.58380 / 0.32 (10174) hydrogen bonds : bond 0.05165 / 3.28 ( 311) hydrogen bonds : angle 4.84675 / 3.40 ( 883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.6407 (mtm-85) cc_final: 0.6178 (mtm-85) REVERT: A 609 SER cc_start: 0.8490 (t) cc_final: 0.7999 (t) REVERT: A 614 SER cc_start: 0.8744 (m) cc_final: 0.8474 (t) REVERT: A 708 GLU cc_start: 0.7164 (tt0) cc_final: 0.6795 (tt0) outliers start: 21 outliers final: 17 residues processed: 112 average time/residue: 0.0691 time to fit residues: 10.2237 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 50.0000 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.195637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156449 restraints weight = 9018.343| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.03 r_work: 0.3660 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7393 Z= 0.148 Angle : 0.526 6.184 10174 Z= 0.290 Chirality : 0.039 0.158 1150 Planarity : 0.003 0.029 1116 Dihedral : 17.380 92.714 1532 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.76 % Allowed : 14.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.31), residues: 737 helix: 0.68 (0.27), residues: 379 sheet: -1.54 (0.58), residues: 73 loop : -1.46 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 481 TYR 0.021 0.002 TYR A 75 PHE 0.014 0.002 PHE A 478 TRP 0.015 0.002 TRP A 33 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 7393) covalent geometry : angle 0.52603 / 0.29 (10174) hydrogen bonds : bond 0.04618 / 2.89 ( 311) hydrogen bonds : angle 4.58746 / 3.21 ( 883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7940 (t80) cc_final: 0.7586 (t80) REVERT: A 88 ASP cc_start: 0.7986 (m-30) cc_final: 0.7635 (m-30) REVERT: A 206 MET cc_start: 0.7442 (tpp) cc_final: 0.6961 (tpp) REVERT: A 218 GLN cc_start: 0.7808 (tt0) cc_final: 0.7555 (tm-30) REVERT: A 391 TYR cc_start: 0.8093 (t80) cc_final: 0.7604 (t80) REVERT: A 609 SER cc_start: 0.8544 (t) cc_final: 0.8220 (t) REVERT: A 614 SER cc_start: 0.8689 (m) cc_final: 0.8434 (t) REVERT: A 640 GLN cc_start: 0.7991 (tt0) cc_final: 0.7072 (tm-30) REVERT: A 708 GLU cc_start: 0.7127 (tt0) cc_final: 0.6745 (tt0) outliers start: 19 outliers final: 16 residues processed: 118 average time/residue: 0.0765 time to fit residues: 11.8502 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.194216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152875 restraints weight = 9081.464| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.14 r_work: 0.3635 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 7393 Z= 0.224 Angle : 0.580 6.661 10174 Z= 0.316 Chirality : 0.041 0.163 1150 Planarity : 0.004 0.044 1116 Dihedral : 17.428 92.137 1532 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.91 % Allowed : 14.53 % Favored : 82.56 % 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: -0.73 (0.31), residues: 737 helix: 0.55 (0.27), residues: 379 sheet: -1.59 (0.57), residues: 73 loop : -1.52 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.024 0.003 TYR A 92 PHE 0.017 0.002 PHE A 637 TRP 0.013 0.002 TRP A 33 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 ( 7393) covalent geometry : angle 0.57950 / 0.32 (10174) hydrogen bonds : bond 0.05004 / 3.17 ( 311) hydrogen bonds : angle 4.74329 / 3.33 ( 883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 206 MET cc_start: 0.7467 (tpp) cc_final: 0.6971 (tpp) REVERT: A 218 GLN cc_start: 0.7783 (tt0) cc_final: 0.7484 (tm-30) REVERT: A 609 SER cc_start: 0.8497 (t) cc_final: 0.8000 (t) REVERT: A 614 SER cc_start: 0.8764 (m) cc_final: 0.8480 (t) REVERT: A 640 GLN cc_start: 0.8072 (tt0) cc_final: 0.7024 (tm-30) REVERT: A 708 GLU cc_start: 0.7158 (tt0) cc_final: 0.6783 (tt0) outliers start: 20 outliers final: 19 residues processed: 111 average time/residue: 0.0767 time to fit residues: 11.2553 Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 57 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.196443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.157454 restraints weight = 9100.189| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.92 r_work: 0.3674 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7393 Z= 0.162 Angle : 0.542 6.253 10174 Z= 0.297 Chirality : 0.039 0.162 1150 Planarity : 0.003 0.029 1116 Dihedral : 17.357 92.880 1532 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.62 % Allowed : 15.12 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.31), residues: 737 helix: 0.62 (0.27), residues: 380 sheet: -1.52 (0.57), residues: 73 loop : -1.45 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.021 0.002 TYR A 454 PHE 0.017 0.002 PHE A 114 TRP 0.013 0.002 TRP A 33 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 7393) covalent geometry : angle 0.54161 / 0.30 (10174) hydrogen bonds : bond 0.04656 / 2.88 ( 311) hydrogen bonds : angle 4.63200 / 3.25 ( 883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7979 (m-30) cc_final: 0.7628 (m-30) REVERT: A 167 ASN cc_start: 0.6513 (OUTLIER) cc_final: 0.6307 (p0) REVERT: A 206 MET cc_start: 0.7473 (tpp) cc_final: 0.7009 (tpp) REVERT: A 218 GLN cc_start: 0.7787 (tt0) cc_final: 0.7553 (tm-30) REVERT: A 391 TYR cc_start: 0.8065 (t80) cc_final: 0.7634 (t80) REVERT: A 614 SER cc_start: 0.8712 (m) cc_final: 0.8474 (t) REVERT: A 708 GLU cc_start: 0.7082 (tt0) cc_final: 0.6712 (tt0) outliers start: 18 outliers final: 17 residues processed: 107 average time/residue: 0.0813 time to fit residues: 11.5466 Evaluate side-chains 111 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 50.0000 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.195263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.154793 restraints weight = 9049.376| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.08 r_work: 0.3655 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7393 Z= 0.208 Angle : 0.571 7.075 10174 Z= 0.312 Chirality : 0.040 0.162 1150 Planarity : 0.004 0.038 1116 Dihedral : 17.370 92.580 1532 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.62 % Allowed : 15.70 % Favored : 81.69 % 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: -0.67 (0.31), residues: 737 helix: 0.57 (0.26), residues: 380 sheet: -1.52 (0.57), residues: 73 loop : -1.49 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.041 0.002 TYR A 454 PHE 0.021 0.002 PHE A 478 TRP 0.014 0.002 TRP A 33 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 7393) covalent geometry : angle 0.57126 / 0.31 (10174) hydrogen bonds : bond 0.04815 / 3.03 ( 311) hydrogen bonds : angle 4.74355 / 3.35 ( 883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7978 (m-30) cc_final: 0.7672 (m-30) REVERT: A 206 MET cc_start: 0.7484 (tpp) cc_final: 0.7000 (tpp) REVERT: A 218 GLN cc_start: 0.7781 (tt0) cc_final: 0.7546 (tm-30) REVERT: A 614 SER cc_start: 0.8815 (m) cc_final: 0.8514 (t) REVERT: A 708 GLU cc_start: 0.7131 (tt0) cc_final: 0.6763 (tt0) outliers start: 18 outliers final: 17 residues processed: 107 average time/residue: 0.0778 time to fit residues: 11.1040 Evaluate side-chains 107 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.0270 chunk 20 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.196330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157579 restraints weight = 9041.757| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.99 r_work: 0.3659 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7393 Z= 0.171 Angle : 0.557 7.093 10174 Z= 0.304 Chirality : 0.040 0.168 1150 Planarity : 0.003 0.028 1116 Dihedral : 17.340 92.928 1532 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.62 % Allowed : 15.84 % Favored : 81.54 % 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 (0.31), residues: 737 helix: 0.63 (0.27), residues: 380 sheet: -1.47 (0.57), residues: 73 loop : -1.45 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 475 TYR 0.033 0.002 TYR A 454 PHE 0.022 0.002 PHE A 478 TRP 0.014 0.002 TRP A 33 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 7393) covalent geometry : angle 0.55701 / 0.30 (10174) hydrogen bonds : bond 0.04692 / 2.92 ( 311) hydrogen bonds : angle 4.68947 / 3.31 ( 883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7980 (m-30) cc_final: 0.7677 (m-30) REVERT: A 206 MET cc_start: 0.7496 (tpp) cc_final: 0.7032 (tpp) REVERT: A 391 TYR cc_start: 0.8064 (t80) cc_final: 0.7648 (t80) REVERT: A 432 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7167 (tptt) REVERT: A 614 SER cc_start: 0.8725 (m) cc_final: 0.8425 (t) outliers start: 18 outliers final: 17 residues processed: 109 average time/residue: 0.0878 time to fit residues: 12.6980 Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 38 optimal weight: 0.0980 chunk 73 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.197223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.159156 restraints weight = 8982.064| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.03 r_work: 0.3688 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7393 Z= 0.132 Angle : 0.546 7.640 10174 Z= 0.298 Chirality : 0.038 0.161 1150 Planarity : 0.003 0.027 1116 Dihedral : 17.267 93.556 1532 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.03 % Allowed : 16.72 % Favored : 81.25 % 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: -0.41 (0.31), residues: 737 helix: 0.83 (0.27), residues: 379 sheet: -1.41 (0.57), residues: 73 loop : -1.43 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 475 TYR 0.018 0.002 TYR A 92 PHE 0.035 0.002 PHE A 460 TRP 0.014 0.001 TRP A 33 HIS 0.002 0.000 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7393) covalent geometry : angle 0.54585 / 0.30 (10174) hydrogen bonds : bond 0.04463 / 2.76 ( 311) hydrogen bonds : angle 4.58716 / 3.24 ( 883) =============================================================================== Job complete usr+sys time: 1434.63 seconds wall clock time: 25 minutes 21.99 seconds (1521.99 seconds total)