Starting phenix.real_space_refine on Thu Jul 2 06:09:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izm_61037/07_2026/9izm_61037.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izm_61037/07_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_61037/07_2026/9izm_61037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izm_61037/07_2026/9izm_61037.map" model { file = "/net/cci-nas-00/data/ceres_data/9izm_61037/07_2026/9izm_61037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izm_61037/07_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-dev-6108/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: 1.38, per 1000 atoms: 0.19 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: 0.47 Conformation dependent library (CDL) restraints added in 328.6 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: 0.87 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: 1.03 Time building geometry restraints manager: 0.65 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: 9783 1.37 - 2.73: 346 2.73 - 4.10: 38 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=" N2 G B -13 " pdb=" C2 G B -13 " pdb=" N3 G B -13 " ideal model delta sigma weight residual 119.90 117.78 2.12 7.00e-01 2.04e+00 9.15e+00 angle pdb=" O2 U B -29 " pdb=" C2 U B -29 " pdb=" N3 U B -29 " ideal model delta sigma weight residual 122.20 120.12 2.08 7.00e-01 2.04e+00 8.80e+00 angle pdb=" C1' G B 0 " pdb=" N9 G B 0 " pdb=" C4 G B 0 " ideal model delta sigma weight residual 126.50 130.00 -3.50 1.30e+00 5.92e-01 7.23e+00 angle pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sigma weight residual 117.70 120.75 -3.05 1.20e+00 6.94e-01 6.48e+00 ... (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 - 0.029: 669 0.029 - 0.058: 333 0.058 - 0.087: 103 0.087 - 0.117: 37 0.117 - 0.146: 8 Chirality restraints: 1150 Sorted by residual: 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=" CA PHE A 637 " pdb=" N PHE A 637 " pdb=" C PHE A 637 " pdb=" CB PHE A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-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: 0.100 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.600 Find NCS groups from input model: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.940 ------------------------------------------------------------------------------- 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= 0.254 Angle : 0.604 6.828 10174 Z= 0.397 Chirality : 0.040 0.146 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 0.00454 / 0.25 ( 7393) covalent geometry : angle 0.60351 / 0.40 (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 : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 PHE cc_start: 0.7883 (m-80) cc_final: 0.7616 (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: 0.0944 time to fit residues: 22.9766 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 : 0.256 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.197674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157839 restraints weight = 9019.185| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.12 r_work: 0.3676 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 7393 Z= 0.165 Angle : 0.589 6.574 10174 Z= 0.328 Chirality : 0.040 0.182 1150 Planarity : 0.004 0.031 1116 Dihedral : 17.675 93.734 1532 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.33 % Allowed : 12.94 % 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: -0.74 (0.30), residues: 737 helix: 0.40 (0.26), residues: 369 sheet: -1.28 (0.57), residues: 71 loop : -1.35 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.017 0.002 TYR A 92 PHE 0.034 0.002 PHE A 222 TRP 0.009 0.002 TRP A 69 HIS 0.010 0.002 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 7393) covalent geometry : angle 0.58875 / 0.33 (10174) hydrogen bonds : bond 0.05691 / 3.69 ( 311) hydrogen bonds : angle 5.04691 / 3.52 ( 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 144 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.6783 (mtm-85) cc_final: 0.6568 (mtm-85) REVERT: A 206 MET cc_start: 0.7379 (tpp) cc_final: 0.7130 (tpp) REVERT: A 211 LEU cc_start: 0.7174 (mt) cc_final: 0.6955 (mt) REVERT: A 212 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6539 (mp0) REVERT: A 227 MET cc_start: 0.8380 (ttm) cc_final: 0.8010 (ttm) REVERT: A 391 TYR cc_start: 0.8035 (t80) cc_final: 0.7607 (t80) REVERT: A 399 LYS cc_start: 0.8233 (tptt) cc_final: 0.8008 (tppt) REVERT: A 589 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: A 606 MET cc_start: 0.8874 (mtm) cc_final: 0.8635 (mtm) REVERT: A 609 SER cc_start: 0.8690 (t) cc_final: 0.8272 (t) REVERT: A 614 SER cc_start: 0.8699 (m) cc_final: 0.8380 (t) REVERT: A 708 GLU cc_start: 0.7002 (tt0) cc_final: 0.6640 (tt0) outliers start: 16 outliers final: 6 residues processed: 138 average time/residue: 0.1006 time to fit residues: 18.1713 Evaluate side-chains 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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: 6.9990 chunk 68 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 487 ASN A 554 GLN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.193685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153455 restraints weight = 8993.226| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.20 r_work: 0.3597 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 7393 Z= 0.292 Angle : 0.635 6.334 10174 Z= 0.351 Chirality : 0.044 0.174 1150 Planarity : 0.005 0.057 1116 Dihedral : 17.677 93.159 1532 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.76 % Allowed : 14.24 % 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: -1.13 (0.30), residues: 737 helix: 0.10 (0.26), residues: 382 sheet: -1.82 (0.55), residues: 73 loop : -1.53 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 197 TYR 0.025 0.003 TYR A 75 PHE 0.031 0.003 PHE A 478 TRP 0.011 0.002 TRP A 268 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.29 ( 7393) covalent geometry : angle 0.63455 / 0.35 (10174) hydrogen bonds : bond 0.05761 / 3.71 ( 311) hydrogen bonds : angle 5.06375 / 3.55 ( 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 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6560 (mp0) REVERT: A 308 TYR cc_start: 0.8017 (p90) cc_final: 0.7635 (p90) REVERT: A 547 LYS cc_start: 0.7527 (mttt) cc_final: 0.7151 (ttpt) REVERT: A 589 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: A 609 SER cc_start: 0.8638 (t) cc_final: 0.8164 (t) REVERT: A 614 SER cc_start: 0.8761 (m) cc_final: 0.8458 (t) REVERT: A 651 LYS cc_start: 0.8390 (pttt) cc_final: 0.7991 (pttm) REVERT: A 708 GLU cc_start: 0.7132 (tt0) cc_final: 0.6744 (tt0) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.1047 time to fit residues: 17.3069 Evaluate side-chains 117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4385 r_free = 0.4385 target = 0.198131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.160113 restraints weight = 9101.951| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.12 r_work: 0.3678 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7393 Z= 0.128 Angle : 0.529 7.048 10174 Z= 0.292 Chirality : 0.039 0.162 1150 Planarity : 0.003 0.029 1116 Dihedral : 17.490 94.154 1532 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.89 % Allowed : 15.12 % 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: -0.66 (0.31), residues: 737 helix: 0.56 (0.26), residues: 381 sheet: -1.55 (0.56), residues: 73 loop : -1.44 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 481 TYR 0.019 0.002 TYR A 454 PHE 0.026 0.002 PHE A 478 TRP 0.007 0.001 TRP A 69 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 7393) covalent geometry : angle 0.52893 / 0.29 (10174) hydrogen bonds : bond 0.04588 / 2.87 ( 311) hydrogen bonds : angle 4.60946 / 3.21 ( 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 125 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7498 (ttm) cc_final: 0.7159 (ttm) REVERT: A 88 ASP cc_start: 0.7965 (m-30) cc_final: 0.7638 (m-30) REVERT: A 155 MET cc_start: 0.7731 (mmm) cc_final: 0.7508 (mmm) REVERT: A 206 MET cc_start: 0.7364 (tpp) cc_final: 0.6874 (tpp) REVERT: A 211 LEU cc_start: 0.6914 (mt) cc_final: 0.6705 (mt) REVERT: A 212 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6397 (mp0) REVERT: A 371 GLU cc_start: 0.7951 (tt0) cc_final: 0.7738 (mt-10) REVERT: A 391 TYR cc_start: 0.8137 (t80) cc_final: 0.7734 (t80) REVERT: A 588 LYS cc_start: 0.7455 (ttpp) cc_final: 0.7177 (ttpp) REVERT: A 589 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: A 609 SER cc_start: 0.8449 (t) cc_final: 0.8108 (t) REVERT: A 614 SER cc_start: 0.8787 (m) cc_final: 0.8438 (t) REVERT: A 651 LYS cc_start: 0.8323 (pttt) cc_final: 0.7970 (pttm) REVERT: A 708 GLU cc_start: 0.6989 (tt0) cc_final: 0.6609 (tt0) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.0992 time to fit residues: 15.6601 Evaluate side-chains 110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 PHE 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 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: 10.0000 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS A 255 ASN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** 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 = 0.193989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153848 restraints weight = 9062.005| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.15 r_work: 0.3600 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2961 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= 0.277 Angle : 0.601 5.956 10174 Z= 0.331 Chirality : 0.043 0.166 1150 Planarity : 0.004 0.055 1116 Dihedral : 17.563 93.254 1532 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.76 % Allowed : 15.41 % Favored : 81.83 % 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: -0.92 (0.30), residues: 737 helix: 0.38 (0.26), residues: 375 sheet: -1.65 (0.57), residues: 75 loop : -1.58 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.025 0.003 TYR A 23 PHE 0.024 0.003 PHE A 478 TRP 0.011 0.003 TRP A 33 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.28 ( 7393) covalent geometry : angle 0.60121 / 0.33 (10174) hydrogen bonds : bond 0.05348 / 3.41 ( 311) hydrogen bonds : angle 4.86356 / 3.42 ( 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 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.7928 (p90) cc_final: 0.7498 (p90) REVERT: A 609 SER cc_start: 0.8608 (t) cc_final: 0.8128 (t) REVERT: A 614 SER cc_start: 0.8742 (m) cc_final: 0.8467 (t) REVERT: A 651 LYS cc_start: 0.8391 (pttt) cc_final: 0.7928 (pttm) REVERT: A 708 GLU cc_start: 0.7127 (tt0) cc_final: 0.6724 (tt0) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.1006 time to fit residues: 15.2675 Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 50.0000 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 581 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.196597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155820 restraints weight = 9011.548| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.13 r_work: 0.3667 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7393 Z= 0.141 Angle : 0.526 6.252 10174 Z= 0.292 Chirality : 0.039 0.159 1150 Planarity : 0.003 0.049 1116 Dihedral : 17.451 93.978 1532 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.03 % Allowed : 15.41 % 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: -0.58 (0.31), residues: 737 helix: 0.65 (0.27), residues: 379 sheet: -1.44 (0.57), residues: 75 loop : -1.45 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.019 0.002 TYR A 454 PHE 0.021 0.002 PHE A 478 TRP 0.016 0.002 TRP A 33 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7393) covalent geometry : angle 0.52557 / 0.29 (10174) hydrogen bonds : bond 0.04588 / 2.85 ( 311) hydrogen bonds : angle 4.55316 / 3.20 ( 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 114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7957 (m-30) cc_final: 0.7621 (m-30) REVERT: A 206 MET cc_start: 0.7444 (tpp) cc_final: 0.6965 (tpp) REVERT: A 217 GLU cc_start: 0.7358 (tp30) cc_final: 0.7078 (mm-30) REVERT: A 391 TYR cc_start: 0.8044 (t80) cc_final: 0.7619 (t80) REVERT: A 588 LYS cc_start: 0.7362 (ttpp) cc_final: 0.7157 (ttpp) REVERT: A 614 SER cc_start: 0.8672 (m) cc_final: 0.8409 (t) REVERT: A 651 LYS cc_start: 0.8335 (pttt) cc_final: 0.7911 (pttm) REVERT: A 708 GLU cc_start: 0.7047 (tt0) cc_final: 0.6647 (tt0) outliers start: 14 outliers final: 13 residues processed: 110 average time/residue: 0.1014 time to fit residues: 14.6309 Evaluate side-chains 107 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 0.0370 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 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 = 0.4364 r_free = 0.4364 target = 0.195731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.156255 restraints weight = 9079.205| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.20 r_work: 0.3648 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 7393 Z= 0.189 Angle : 0.552 9.554 10174 Z= 0.303 Chirality : 0.040 0.167 1150 Planarity : 0.003 0.035 1116 Dihedral : 17.432 93.964 1532 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.62 % Allowed : 14.53 % Favored : 82.85 % 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: -0.55 (0.31), residues: 737 helix: 0.70 (0.27), residues: 380 sheet: -1.44 (0.57), residues: 75 loop : -1.48 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.031 0.002 TYR A 454 PHE 0.021 0.002 PHE A 478 TRP 0.016 0.002 TRP A 33 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 7393) covalent geometry : angle 0.55209 / 0.30 (10174) hydrogen bonds : bond 0.04737 / 2.99 ( 311) hydrogen bonds : angle 4.62174 / 3.25 ( 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 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7995 (m-30) cc_final: 0.7656 (m-30) REVERT: A 206 MET cc_start: 0.7463 (tpp) cc_final: 0.6955 (tpp) REVERT: A 391 TYR cc_start: 0.8133 (t80) cc_final: 0.7683 (t80) REVERT: A 588 LYS cc_start: 0.7395 (ttpp) cc_final: 0.7186 (ttpp) REVERT: A 614 SER cc_start: 0.8746 (m) cc_final: 0.8463 (t) REVERT: A 651 LYS cc_start: 0.8329 (pttt) cc_final: 0.7889 (pttm) REVERT: A 708 GLU cc_start: 0.7119 (tt0) cc_final: 0.6717 (tt0) outliers start: 18 outliers final: 14 residues processed: 110 average time/residue: 0.1010 time to fit residues: 14.5676 Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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 621 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 711 VAL 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: 6.9990 chunk 67 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.196001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156448 restraints weight = 9118.379| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.98 r_work: 0.3665 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7393 Z= 0.190 Angle : 0.546 7.641 10174 Z= 0.301 Chirality : 0.039 0.164 1150 Planarity : 0.003 0.035 1116 Dihedral : 17.428 93.926 1532 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.33 % Allowed : 14.39 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.31), residues: 737 helix: 0.75 (0.27), residues: 379 sheet: -1.45 (0.57), residues: 75 loop : -1.46 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 475 TYR 0.027 0.002 TYR A 454 PHE 0.034 0.002 PHE A 460 TRP 0.015 0.002 TRP A 33 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 7393) covalent geometry : angle 0.54594 / 0.30 (10174) hydrogen bonds : bond 0.04724 / 2.96 ( 311) hydrogen bonds : angle 4.62521 / 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 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8292 (t80) cc_final: 0.7956 (t80) REVERT: A 88 ASP cc_start: 0.7969 (m-30) cc_final: 0.7637 (m-30) REVERT: A 167 ASN cc_start: 0.6327 (OUTLIER) cc_final: 0.6078 (p0) REVERT: A 206 MET cc_start: 0.7497 (tpp) cc_final: 0.7010 (tpp) REVERT: A 217 GLU cc_start: 0.7407 (tp30) cc_final: 0.6680 (mm-30) REVERT: A 391 TYR cc_start: 0.8065 (t80) cc_final: 0.7641 (t80) REVERT: A 454 TYR cc_start: 0.8319 (t80) cc_final: 0.8075 (t80) REVERT: A 614 SER cc_start: 0.8715 (m) cc_final: 0.8465 (t) REVERT: A 651 LYS cc_start: 0.8388 (pttt) cc_final: 0.7968 (pttm) REVERT: A 708 GLU cc_start: 0.7129 (tt0) cc_final: 0.6744 (tt0) outliers start: 16 outliers final: 15 residues processed: 106 average time/residue: 0.0998 time to fit residues: 14.0318 Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 50.0000 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.195461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155911 restraints weight = 8993.096| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.12 r_work: 0.3640 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3397 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= 0.178 Angle : 0.542 7.215 10174 Z= 0.297 Chirality : 0.039 0.160 1150 Planarity : 0.003 0.032 1116 Dihedral : 17.409 93.986 1532 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.18 % Allowed : 15.12 % 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: -0.44 (0.31), residues: 737 helix: 0.79 (0.27), residues: 379 sheet: -1.40 (0.56), residues: 75 loop : -1.42 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 475 TYR 0.025 0.002 TYR A 454 PHE 0.029 0.002 PHE A 460 TRP 0.015 0.002 TRP A 33 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 7393) covalent geometry : angle 0.54163 / 0.30 (10174) hydrogen bonds : bond 0.04660 / 2.92 ( 311) hydrogen bonds : angle 4.61771 / 3.25 ( 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 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8298 (t80) cc_final: 0.7975 (t80) REVERT: A 88 ASP cc_start: 0.7958 (m-30) cc_final: 0.7633 (m-30) REVERT: A 206 MET cc_start: 0.7495 (tpp) cc_final: 0.6998 (tpp) REVERT: A 217 GLU cc_start: 0.7367 (tp30) cc_final: 0.6574 (mm-30) REVERT: A 391 TYR cc_start: 0.8069 (t80) cc_final: 0.7645 (t80) REVERT: A 614 SER cc_start: 0.8828 (m) cc_final: 0.8500 (t) REVERT: A 651 LYS cc_start: 0.8360 (pttt) cc_final: 0.7941 (pttm) REVERT: A 708 GLU cc_start: 0.7135 (tt0) cc_final: 0.6748 (tt0) outliers start: 15 outliers final: 14 residues processed: 106 average time/residue: 0.0999 time to fit residues: 14.0633 Evaluate side-chains 107 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 621 LEU 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: 0.6980 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.197210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156937 restraints weight = 9056.143| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.09 r_work: 0.3680 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7393 Z= 0.153 Angle : 0.529 6.869 10174 Z= 0.289 Chirality : 0.038 0.162 1150 Planarity : 0.003 0.029 1116 Dihedral : 17.349 94.509 1532 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.33 % Allowed : 15.26 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.31 (0.31), residues: 737 helix: 0.89 (0.27), residues: 379 sheet: -1.28 (0.56), residues: 75 loop : -1.37 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 474 TYR 0.020 0.002 TYR A 75 PHE 0.030 0.002 PHE A 460 TRP 0.015 0.002 TRP A 33 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7393) covalent geometry : angle 0.52861 / 0.29 (10174) hydrogen bonds : bond 0.04495 / 2.81 ( 311) hydrogen bonds : angle 4.55063 / 3.21 ( 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 116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7287 (mptt) cc_final: 0.7084 (ttpp) REVERT: A 49 PHE cc_start: 0.8300 (t80) cc_final: 0.7990 (t80) REVERT: A 88 ASP cc_start: 0.7933 (m-30) cc_final: 0.7630 (m-30) REVERT: A 206 MET cc_start: 0.7496 (tpp) cc_final: 0.7003 (tpp) REVERT: A 217 GLU cc_start: 0.7351 (tp30) cc_final: 0.6573 (mm-30) REVERT: A 316 ASN cc_start: 0.7433 (t0) cc_final: 0.7127 (t0) REVERT: A 391 TYR cc_start: 0.7983 (t80) cc_final: 0.7631 (t80) REVERT: A 614 SER cc_start: 0.8681 (m) cc_final: 0.8404 (t) REVERT: A 651 LYS cc_start: 0.8354 (pttt) cc_final: 0.7927 (pttm) REVERT: A 708 GLU cc_start: 0.7099 (tt0) cc_final: 0.6735 (tt0) outliers start: 16 outliers final: 14 residues processed: 108 average time/residue: 0.1020 time to fit residues: 14.4838 Evaluate side-chains 110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 197 ARG 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 504 LEU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 621 LEU 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: 0.9980 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** 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 = 0.4395 r_free = 0.4395 target = 0.198847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.158711 restraints weight = 9073.654| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.11 r_work: 0.3704 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7393 Z= 0.126 Angle : 0.528 7.931 10174 Z= 0.290 Chirality : 0.038 0.163 1150 Planarity : 0.003 0.028 1116 Dihedral : 17.270 95.148 1532 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.74 % Allowed : 15.70 % 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: -0.19 (0.31), residues: 737 helix: 0.98 (0.27), residues: 379 sheet: -1.15 (0.56), residues: 75 loop : -1.33 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 474 TYR 0.025 0.002 TYR A 92 PHE 0.023 0.002 PHE A 637 TRP 0.016 0.001 TRP A 33 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 7393) covalent geometry : angle 0.52814 / 0.29 (10174) hydrogen bonds : bond 0.04309 / 2.67 ( 311) hydrogen bonds : angle 4.45107 / 3.14 ( 883) =============================================================================== Job complete usr+sys time: 1834.97 seconds wall clock time: 32 minutes 32.65 seconds (1952.65 seconds total)