Starting phenix.real_space_refine on Wed Sep 17 08:27:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izm_61037/09_2025/9izm_61037.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izm_61037/09_2025/9izm_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 { model { file = "/net/cci-nas-00/data/ceres_data/9izm_61037/09_2025/9izm_61037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izm_61037/09_2025/9izm_61037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9izm_61037/09_2025/9izm_61037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izm_61037/09_2025/9izm_61037.map" } 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-2.0-5805/lib/python3.9/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: 1.97, per 1000 atoms: 0.28 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: 0.64 Conformation dependent library (CDL) restraints added in 325.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.09 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: 1.20 Time building geometry restraints manager: 0.86 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=" CG1 ILE A 216 " pdb=" CD1 ILE A 216 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.49e+00 bond pdb=" CB ILE A 5 " pdb=" CG2 ILE A 5 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.09e+00 bond pdb=" CG LEU A 490 " pdb=" CD1 LEU A 490 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CA ASP A 338 " pdb=" C ASP A 338 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.10e-02 8.26e+03 1.01e+00 bond pdb=" CG1 ILE A 522 " pdb=" CD1 ILE A 522 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.00e+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=" C CYS A 398 " pdb=" N LYS A 399 " pdb=" CA LYS A 399 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" CA ASN A 419 " pdb=" C ASN A 419 " pdb=" N ARG A 420 " ideal model delta sigma weight residual 115.67 118.49 -2.82 1.23e+00 6.61e-01 5.25e+00 angle pdb=" CA PHE A 637 " pdb=" CB PHE A 637 " pdb=" CG PHE A 637 " ideal model delta sigma weight residual 113.80 116.06 -2.26 1.00e+00 1.00e+00 5.13e+00 angle pdb=" C ASN A 581 " pdb=" N ASN A 582 " pdb=" CA ASN A 582 " ideal model delta sigma weight residual 121.54 125.84 -4.30 1.91e+00 2.74e-01 5.06e+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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.630 Find NCS groups from input model: 0.020 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 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= 0.208 Angle : 0.603 6.828 10174 Z= 0.350 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 aren 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 covalent geometry : bond 0.00454 ( 7393) covalent geometry : angle 0.60349 (10174) hydrogen bonds : bond 0.18302 ( 311) hydrogen bonds : angle 6.59418 ( 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 : 0.252 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: 0.1056 time to fit residues: 25.3233 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 : 0.247 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN A 297 ASN A 402 GLN A 509 ASN A 554 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.198569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158671 restraints weight = 9026.356| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.07 r_work: 0.3687 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2499 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= 0.144 Angle : 0.533 6.826 10174 Z= 0.292 Chirality : 0.038 0.184 1150 Planarity : 0.003 0.030 1116 Dihedral : 17.414 94.711 1532 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.18 % Allowed : 12.06 % Favored : 85.76 % 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 aren not related in a simple way. whole: -0.61 (0.31), residues: 737 helix: 0.55 (0.27), residues: 380 sheet: -1.35 (0.56), residues: 73 loop : -1.38 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.020 0.002 TYR A 75 PHE 0.035 0.002 PHE A 222 TRP 0.007 0.001 TRP A 268 HIS 0.008 0.001 HIS A 726 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7393) covalent geometry : angle 0.53312 (10174) hydrogen bonds : bond 0.04628 ( 311) hydrogen bonds : angle 4.78555 ( 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 147 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8185 (mtmm) REVERT: A 206 MET cc_start: 0.7370 (tpp) cc_final: 0.6913 (tpp) REVERT: A 212 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6311 (mp0) REVERT: A 371 GLU cc_start: 0.7778 (tt0) cc_final: 0.7507 (mt-10) REVERT: A 391 TYR cc_start: 0.8046 (t80) cc_final: 0.7588 (t80) REVERT: A 589 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: A 609 SER cc_start: 0.8254 (t) cc_final: 0.7920 (t) REVERT: A 614 SER cc_start: 0.8745 (m) cc_final: 0.8430 (t) REVERT: A 640 GLN cc_start: 0.7918 (tt0) cc_final: 0.7128 (tm-30) REVERT: A 651 LYS cc_start: 0.8320 (pttt) cc_final: 0.8056 (pttt) REVERT: A 708 GLU cc_start: 0.7054 (tt0) cc_final: 0.6733 (tt0) outliers start: 15 outliers final: 6 residues processed: 142 average time/residue: 0.0998 time to fit residues: 18.6758 Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.196086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156039 restraints weight = 8986.777| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.19 r_work: 0.3662 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2988 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= 0.199 Angle : 0.559 7.376 10174 Z= 0.301 Chirality : 0.040 0.169 1150 Planarity : 0.004 0.037 1116 Dihedral : 17.442 93.479 1532 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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 aren not related in a simple way. whole: -0.70 (0.30), residues: 737 helix: 0.48 (0.26), residues: 378 sheet: -1.46 (0.56), residues: 73 loop : -1.39 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.026 0.002 TYR A 75 PHE 0.031 0.002 PHE A 478 TRP 0.009 0.002 TRP A 33 HIS 0.003 0.001 HIS A 646 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 7393) covalent geometry : angle 0.55939 (10174) hydrogen bonds : bond 0.04829 ( 311) hydrogen bonds : angle 4.71131 ( 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 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7437 (tpp) cc_final: 0.6958 (tpp) REVERT: A 217 GLU cc_start: 0.7305 (tp30) cc_final: 0.6993 (mm-30) REVERT: A 391 TYR cc_start: 0.8106 (t80) cc_final: 0.7652 (t80) REVERT: A 588 LYS cc_start: 0.7512 (ttpp) cc_final: 0.7106 (tttp) REVERT: A 614 SER cc_start: 0.8797 (m) cc_final: 0.8510 (t) REVERT: A 640 GLN cc_start: 0.7951 (tt0) cc_final: 0.7048 (tm-30) REVERT: A 708 GLU cc_start: 0.7023 (tt0) cc_final: 0.6708 (tt0) outliers start: 15 outliers final: 10 residues processed: 118 average time/residue: 0.1084 time to fit residues: 16.6286 Evaluate side-chains 105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 66 optimal weight: 0.0020 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4373 r_free = 0.4373 target = 0.196853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.156008 restraints weight = 9103.631| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.07 r_work: 0.3665 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7393 Z= 0.170 Angle : 0.531 5.850 10174 Z= 0.286 Chirality : 0.039 0.165 1150 Planarity : 0.003 0.031 1116 Dihedral : 17.348 93.952 1532 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.47 % Allowed : 13.52 % Favored : 84.01 % 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 aren not related in a simple way. whole: -0.51 (0.31), residues: 737 helix: 0.66 (0.27), residues: 380 sheet: -1.44 (0.57), residues: 73 loop : -1.34 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 481 TYR 0.020 0.002 TYR A 75 PHE 0.022 0.002 PHE A 478 TRP 0.011 0.002 TRP A 33 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7393) covalent geometry : angle 0.53131 (10174) hydrogen bonds : bond 0.04475 ( 311) hydrogen bonds : angle 4.54730 ( 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: 17 poor density : 108 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 ASN cc_start: 0.6451 (t160) cc_final: 0.6157 (p0) REVERT: A 206 MET cc_start: 0.7502 (tpp) cc_final: 0.7024 (tpp) REVERT: A 391 TYR cc_start: 0.8039 (t80) cc_final: 0.7593 (t80) REVERT: A 471 MET cc_start: 0.7488 (mmt) cc_final: 0.7260 (mmt) REVERT: A 614 SER cc_start: 0.8726 (m) cc_final: 0.8476 (t) REVERT: A 640 GLN cc_start: 0.7943 (tt0) cc_final: 0.7008 (tm-30) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.1010 time to fit residues: 15.7177 Evaluate side-chains 107 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 247 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.191888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151531 restraints weight = 9102.841| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.12 r_work: 0.3598 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 7393 Z= 0.349 Angle : 0.691 6.697 10174 Z= 0.363 Chirality : 0.045 0.162 1150 Planarity : 0.005 0.058 1116 Dihedral : 17.720 94.843 1532 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.63 % Allowed : 15.26 % Favored : 81.10 % 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 aren not related in a simple way. whole: -0.99 (0.30), residues: 737 helix: 0.23 (0.26), residues: 386 sheet: -1.59 (0.58), residues: 73 loop : -1.56 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 667 TYR 0.026 0.003 TYR A 23 PHE 0.021 0.003 PHE A 478 TRP 0.008 0.002 TRP A 69 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00793 ( 7393) covalent geometry : angle 0.69088 (10174) hydrogen bonds : bond 0.05595 ( 311) hydrogen bonds : angle 5.01924 ( 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 125 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 ASN cc_start: 0.6700 (t160) cc_final: 0.6398 (p0) REVERT: A 206 MET cc_start: 0.7511 (tpp) cc_final: 0.7014 (tpp) REVERT: A 308 TYR cc_start: 0.7958 (p90) cc_final: 0.7614 (p90) REVERT: A 545 LEU cc_start: 0.8345 (tp) cc_final: 0.8113 (tp) REVERT: A 609 SER cc_start: 0.8595 (t) cc_final: 0.8079 (t) REVERT: A 640 GLN cc_start: 0.8083 (tt0) cc_final: 0.7067 (tm-30) REVERT: A 708 GLU cc_start: 0.7927 (mp0) cc_final: 0.7501 (mp0) outliers start: 25 outliers final: 18 residues processed: 117 average time/residue: 0.1016 time to fit residues: 15.6465 Evaluate side-chains 110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 GLU 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 387 LEU Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 675 ASN 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: 1.9990 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 50.0000 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4378 r_free = 0.4378 target = 0.197224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157638 restraints weight = 9053.261| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.00 r_work: 0.3672 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7393 Z= 0.136 Angle : 0.525 8.478 10174 Z= 0.278 Chirality : 0.038 0.171 1150 Planarity : 0.003 0.029 1116 Dihedral : 17.289 94.968 1532 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.33 % Allowed : 16.42 % 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 aren not related in a simple way. whole: -0.41 (0.31), residues: 737 helix: 0.80 (0.27), residues: 386 sheet: -1.41 (0.57), residues: 75 loop : -1.43 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 474 TYR 0.019 0.002 TYR A 60 PHE 0.017 0.002 PHE A 478 TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7393) covalent geometry : angle 0.52516 (10174) hydrogen bonds : bond 0.04229 ( 311) hydrogen bonds : angle 4.53291 ( 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 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8056 (t80) cc_final: 0.7713 (t80) REVERT: A 88 ASP cc_start: 0.7941 (m-30) cc_final: 0.7626 (m-30) REVERT: A 167 ASN cc_start: 0.6800 (t0) cc_final: 0.6418 (p0) REVERT: A 391 TYR cc_start: 0.8017 (t80) cc_final: 0.7697 (t80) REVERT: A 614 SER cc_start: 0.8690 (m) cc_final: 0.8380 (t) REVERT: A 708 GLU cc_start: 0.7934 (mp0) cc_final: 0.7633 (mp0) outliers start: 16 outliers final: 12 residues processed: 111 average time/residue: 0.0956 time to fit residues: 14.0699 Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 247 GLU 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 589 TYR Chi-restraints excluded: chain A residue 608 LYS 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: 0.9990 chunk 46 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 316 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4363 r_free = 0.4363 target = 0.195661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.154527 restraints weight = 9048.135| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.09 r_work: 0.3645 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7393 Z= 0.177 Angle : 0.548 7.345 10174 Z= 0.291 Chirality : 0.039 0.160 1150 Planarity : 0.003 0.032 1116 Dihedral : 17.293 94.904 1532 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.74 % Allowed : 16.72 % 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 aren not related in a simple way. whole: -0.37 (0.31), residues: 737 helix: 0.85 (0.27), residues: 387 sheet: -1.43 (0.58), residues: 75 loop : -1.42 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.018 0.002 TYR A 75 PHE 0.016 0.002 PHE A 478 TRP 0.006 0.001 TRP A 33 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7393) covalent geometry : angle 0.54807 (10174) hydrogen bonds : bond 0.04488 ( 311) hydrogen bonds : angle 4.57176 ( 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 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8001 (t80) cc_final: 0.7413 (t80) REVERT: A 167 ASN cc_start: 0.6748 (t0) cc_final: 0.6435 (p0) REVERT: A 206 MET cc_start: 0.7501 (tpp) cc_final: 0.6965 (tpp) REVERT: A 391 TYR cc_start: 0.8070 (t80) cc_final: 0.7677 (t80) REVERT: A 589 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: A 614 SER cc_start: 0.8639 (m) cc_final: 0.8318 (t) REVERT: A 708 GLU cc_start: 0.7915 (mp0) cc_final: 0.7673 (mp0) outliers start: 12 outliers final: 9 residues processed: 108 average time/residue: 0.1007 time to fit residues: 14.2782 Evaluate side-chains 103 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 247 GLU 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 589 TYR 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: 6.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** 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 = 0.4361 r_free = 0.4361 target = 0.195436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.154546 restraints weight = 9084.341| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.06 r_work: 0.3643 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7393 Z= 0.189 Angle : 0.566 8.512 10174 Z= 0.301 Chirality : 0.040 0.175 1150 Planarity : 0.003 0.034 1116 Dihedral : 17.258 95.351 1532 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.89 % Allowed : 16.42 % 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 aren not related in a simple way. whole: -0.30 (0.31), residues: 737 helix: 0.91 (0.27), residues: 387 sheet: -1.25 (0.60), residues: 73 loop : -1.46 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 474 TYR 0.018 0.002 TYR A 92 PHE 0.015 0.002 PHE A 478 TRP 0.007 0.001 TRP A 33 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7393) covalent geometry : angle 0.56642 (10174) hydrogen bonds : bond 0.04545 ( 311) hydrogen bonds : angle 4.59306 ( 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 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7960 (t80) cc_final: 0.7663 (t80) REVERT: A 167 ASN cc_start: 0.6641 (t0) cc_final: 0.6380 (p0) REVERT: A 206 MET cc_start: 0.7550 (tpp) cc_final: 0.7028 (tpp) REVERT: A 391 TYR cc_start: 0.8057 (t80) cc_final: 0.7655 (t80) REVERT: A 589 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6536 (m-80) REVERT: A 609 SER cc_start: 0.8436 (t) cc_final: 0.7969 (t) outliers start: 13 outliers final: 11 residues processed: 109 average time/residue: 0.0985 time to fit residues: 14.1686 Evaluate side-chains 104 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS 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: 4.9990 chunk 22 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 50.0000 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 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 = 0.4377 r_free = 0.4377 target = 0.196833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156167 restraints weight = 9008.927| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.07 r_work: 0.3673 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7393 Z= 0.160 Angle : 0.557 7.403 10174 Z= 0.296 Chirality : 0.039 0.186 1150 Planarity : 0.003 0.029 1116 Dihedral : 17.155 95.957 1532 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 17.01 % 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 aren not related in a simple way. whole: -0.22 (0.31), residues: 737 helix: 1.00 (0.27), residues: 387 sheet: -1.28 (0.58), residues: 75 loop : -1.42 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.019 0.002 TYR A 548 PHE 0.015 0.002 PHE A 478 TRP 0.008 0.001 TRP A 33 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7393) covalent geometry : angle 0.55738 (10174) hydrogen bonds : bond 0.04320 ( 311) hydrogen bonds : angle 4.51554 ( 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: 12 poor density : 100 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7990 (t80) cc_final: 0.7706 (t80) REVERT: A 88 ASP cc_start: 0.7936 (m-30) cc_final: 0.7615 (m-30) REVERT: A 206 MET cc_start: 0.7528 (tpp) cc_final: 0.6993 (tpp) REVERT: A 391 TYR cc_start: 0.8007 (t80) cc_final: 0.7630 (t80) REVERT: A 589 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: A 614 SER cc_start: 0.8597 (m) cc_final: 0.8291 (t) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.0966 time to fit residues: 13.7472 Evaluate side-chains 102 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** A 581 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 = 0.4342 r_free = 0.4342 target = 0.193603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152985 restraints weight = 9049.947| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.87 r_work: 0.3626 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7393 Z= 0.250 Angle : 0.633 7.099 10174 Z= 0.336 Chirality : 0.042 0.202 1150 Planarity : 0.004 0.044 1116 Dihedral : 17.281 94.772 1532 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.74 % Allowed : 17.01 % 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 aren not related in a simple way. whole: -0.54 (0.31), residues: 737 helix: 0.70 (0.26), residues: 387 sheet: -1.40 (0.57), residues: 75 loop : -1.54 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.022 0.002 TYR A 23 PHE 0.015 0.002 PHE A 478 TRP 0.007 0.001 TRP A 33 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 7393) covalent geometry : angle 0.63334 (10174) hydrogen bonds : bond 0.04989 ( 311) hydrogen bonds : angle 4.76940 ( 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 103 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8015 (t80) cc_final: 0.7711 (t80) REVERT: A 206 MET cc_start: 0.7495 (tpp) cc_final: 0.6938 (tpp) REVERT: A 589 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: A 609 SER cc_start: 0.8473 (t) cc_final: 0.7947 (t) REVERT: A 640 GLN cc_start: 0.8011 (tt0) cc_final: 0.6957 (tm-30) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.0963 time to fit residues: 12.5613 Evaluate side-chains 103 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 589 TYR 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: 8.9990 chunk 27 optimal weight: 0.0050 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 264 GLN A 646 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.202021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.163562 restraints weight = 9061.347| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.02 r_work: 0.3750 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7393 Z= 0.112 Angle : 0.541 8.482 10174 Z= 0.285 Chirality : 0.037 0.181 1150 Planarity : 0.003 0.028 1116 Dihedral : 16.807 97.709 1532 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.31 % Allowed : 18.17 % Favored : 80.52 % 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 aren not related in a simple way. whole: 0.03 (0.32), residues: 737 helix: 1.20 (0.27), residues: 388 sheet: -1.08 (0.54), residues: 85 loop : -1.33 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.014 0.001 TYR A 548 PHE 0.016 0.001 PHE A 478 TRP 0.007 0.001 TRP A 268 HIS 0.002 0.000 HIS A 646 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7393) covalent geometry : angle 0.54098 (10174) hydrogen bonds : bond 0.03781 ( 311) hydrogen bonds : angle 4.33004 ( 883) =============================================================================== Job complete usr+sys time: 1878.66 seconds wall clock time: 33 minutes 2.00 seconds (1982.00 seconds total)