Starting phenix.real_space_refine on Tue Aug 4 21:18:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9i_64873/08_2026/9v9i_64873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9i_64873/08_2026/9v9i_64873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9i_64873/08_2026/9v9i_64873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9i_64873/08_2026/9v9i_64873.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9i_64873/08_2026/9v9i_64873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9i_64873/08_2026/9v9i_64873.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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 33 5.49 5 Mg 2 5.21 5 S 15 5.16 5 C 4116 2.51 5 N 1219 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6716 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 6015 Classifications: {'peptide': 756} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 42, 'TRANS': 713} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.55, per 1000 atoms: 0.23 Number of scatterers: 6716 At special positions: 0 Unit cell: (79.143, 99.567, 101.269, 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 15 16.00 P 33 15.00 Mg 2 11.99 O 1331 8.00 N 1219 7.00 C 4116 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: 0.49 Conformation dependent library (CDL) restraints added in 289.0 milliseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 32.0% alpha, 22.0% beta 4 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.755A pdb=" N ARG A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 131 removed outlier: 3.667A pdb=" N ALA A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.412A pdb=" N MET A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 removed outlier: 3.673A pdb=" N GLY A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 482 through 491 removed outlier: 3.806A pdb=" N LEU A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 516 through 531 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.594A pdb=" N PHE A 344 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.664A pdb=" N LEU A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 330 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.625A pdb=" N THR A 60 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 67 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 68 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 70 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 23 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A 99 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 25 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 239 removed outlier: 6.657A pdb=" N PHE A 274 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER A 235 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA A 272 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA8, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.987A pdb=" N LEU A 402 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN A 439 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 404 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP A 401 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 472 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL A 403 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 474 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 405 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 568 through 575 removed outlier: 3.543A pdb=" N ASP A 550 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE A 545 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N HIS A 615 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET A 547 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASP A 617 " --> pdb=" O MET A 547 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 549 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 649 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER A 679 " --> pdb=" O THR A 691 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 0.88 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: 1858 1.33 - 1.45: 1300 1.45 - 1.57: 3674 1.57 - 1.69: 64 1.69 - 1.81: 23 Bond restraints: 6919 Sorted by residual: bond pdb=" C GLU A 673 " pdb=" N ASN A 674 " ideal model delta sigma weight residual 1.330 1.416 -0.086 1.47e-02 4.63e+03 3.44e+01 bond pdb=" N MET A 311 " pdb=" CA MET A 311 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.18e-02 7.18e+03 7.85e+00 bond pdb=" N ASP A 408 " pdb=" CA ASP A 408 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.30e-02 5.92e+03 7.25e+00 bond pdb=" N SER A 109 " pdb=" CA SER A 109 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.34e-02 5.57e+03 5.84e+00 bond pdb=" N VAL A 308 " pdb=" CA VAL A 308 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.23e-02 6.61e+03 5.24e+00 ... (remaining 6914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 9109 1.64 - 3.28: 376 3.28 - 4.91: 47 4.91 - 6.55: 6 6.55 - 8.19: 3 Bond angle restraints: 9541 Sorted by residual: angle pdb=" O4' DG B 4 " pdb=" C4' DG B 4 " pdb=" C3' DG B 4 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT B 13 " pdb=" C4 DT B 13 " pdb=" O4 DT B 13 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B 1 " pdb=" C4 DT B 1 " pdb=" O4 DT B 1 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT B 16 " pdb=" C4 DT B 16 " pdb=" O4 DT B 16 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 9536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.99: 3917 27.99 - 55.97: 185 55.97 - 83.96: 21 83.96 - 111.95: 0 111.95 - 139.94: 1 Dihedral angle restraints: 4124 sinusoidal: 1944 harmonic: 2180 Sorted by residual: dihedral pdb=" C4' DG B 12 " pdb=" C3' DG B 12 " pdb=" O3' DG B 12 " pdb=" P DT B 13 " ideal model delta sinusoidal sigma weight residual 220.00 80.06 139.94 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA HIS A 206 " pdb=" C HIS A 206 " pdb=" N VAL A 207 " pdb=" CA VAL A 207 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TYR A 543 " pdb=" C TYR A 543 " pdb=" N ASP A 544 " pdb=" CA ASP A 544 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 826 0.047 - 0.095: 159 0.095 - 0.142: 75 0.142 - 0.189: 6 0.189 - 0.236: 1 Chirality restraints: 1067 Sorted by residual: chirality pdb=" CA GLN A 310 " pdb=" N GLN A 310 " pdb=" C GLN A 310 " pdb=" CB GLN A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA LEU A 405 " pdb=" N LEU A 405 " pdb=" C LEU A 405 " pdb=" CB LEU A 405 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA GLU A 634 " pdb=" N GLU A 634 " pdb=" C GLU A 634 " pdb=" CB GLU A 634 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1064 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 284 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 285 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 716 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 717 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 107 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C SER A 107 " -0.030 2.00e-02 2.50e+03 pdb=" O SER A 107 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 108 " 0.010 2.00e-02 2.50e+03 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 91 2.64 - 3.21: 5647 3.21 - 3.77: 9923 3.77 - 4.34: 14568 4.34 - 4.90: 23271 Nonbonded interactions: 53500 Sorted by model distance: nonbonded pdb=" OE1 GLN A 497 " pdb="MG MG A 801 " model vdw 2.080 2.170 nonbonded pdb=" OD2 ASP A 550 " pdb="MG MG A 802 " model vdw 2.120 2.170 nonbonded pdb=" OP2 DT B 1 " pdb="MG MG A 801 " model vdw 2.234 2.170 nonbonded pdb=" OD1 ASP A 550 " pdb="MG MG A 802 " model vdw 2.287 2.170 nonbonded pdb=" OH TYR A 546 " pdb=" OD2 ASP A 730 " model vdw 2.305 3.040 ... (remaining 53495 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: 1.510 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.570 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:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 : 0.004 0.086 6919 Z= 0.269 Angle : 0.716 8.190 9541 Z= 0.460 Chirality : 0.047 0.236 1067 Planarity : 0.006 0.066 1133 Dihedral : 15.241 139.936 2720 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.47 % Allowed : 0.93 % Favored : 98.60 % 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: 0.18 (0.30), residues: 754 helix: 0.79 (0.36), residues: 218 sheet: -0.07 (0.38), residues: 202 loop : -0.05 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.014 0.002 TYR A 257 PHE 0.017 0.002 PHE A 159 TRP 0.010 0.001 TRP A 620 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.27 ( 6919) covalent geometry : angle 0.71621 / 0.46 ( 9541) hydrogen bonds : bond 0.21922 / 14.93 ( 260) hydrogen bonds : angle 8.16204 / 5.86 ( 736) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.173 Fit side-chains REVERT: A 484 TYR cc_start: 0.6933 (t80) cc_final: 0.6647 (t80) REVERT: A 654 LYS cc_start: 0.7451 (tptt) cc_final: 0.6812 (mttt) outliers start: 3 outliers final: 0 residues processed: 90 average time/residue: 0.7135 time to fit residues: 66.9500 Evaluate side-chains 56 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.192869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148603 restraints weight = 7602.631| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.01 r_work: 0.3426 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6919 Z= 0.134 Angle : 0.579 6.929 9541 Z= 0.313 Chirality : 0.042 0.156 1067 Planarity : 0.005 0.058 1133 Dihedral : 14.827 140.541 1256 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.56 % Allowed : 8.86 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.31), residues: 754 helix: 1.31 (0.36), residues: 224 sheet: 0.17 (0.39), residues: 198 loop : -0.17 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 490 TYR 0.013 0.001 TYR A 257 PHE 0.012 0.001 PHE A 245 TRP 0.013 0.001 TRP A 570 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 6919) covalent geometry : angle 0.57918 / 0.31 ( 9541) hydrogen bonds : bond 0.05257 / 3.62 ( 260) hydrogen bonds : angle 5.78863 / 4.27 ( 736) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.236 Fit side-chains REVERT: A 27 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6011 (tmm-80) REVERT: A 255 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6242 (tpt-90) REVERT: A 349 ARG cc_start: 0.7628 (tpt170) cc_final: 0.7369 (tpt170) REVERT: A 484 TYR cc_start: 0.6955 (t80) cc_final: 0.6439 (t80) REVERT: A 485 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: A 654 LYS cc_start: 0.7338 (tptt) cc_final: 0.6635 (mttt) REVERT: A 758 ARG cc_start: 0.6690 (mmm160) cc_final: 0.5552 (mmt180) outliers start: 10 outliers final: 2 residues processed: 69 average time/residue: 0.6178 time to fit residues: 44.8192 Evaluate side-chains 61 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 485 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 ASN A 646 GLN A 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.189159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144601 restraints weight = 7562.804| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.01 r_work: 0.3388 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6919 Z= 0.147 Angle : 0.563 6.974 9541 Z= 0.301 Chirality : 0.043 0.182 1067 Planarity : 0.005 0.050 1133 Dihedral : 14.857 139.586 1256 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.49 % Allowed : 9.33 % Favored : 88.18 % 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: 0.43 (0.31), residues: 754 helix: 1.42 (0.35), residues: 224 sheet: 0.01 (0.40), residues: 188 loop : -0.22 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 435 TYR 0.012 0.001 TYR A 380 PHE 0.012 0.001 PHE A 232 TRP 0.012 0.001 TRP A 570 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6919) covalent geometry : angle 0.56270 / 0.30 ( 9541) hydrogen bonds : bond 0.04441 / 3.03 ( 260) hydrogen bonds : angle 5.23682 / 3.83 ( 736) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.254 Fit side-chains REVERT: A 27 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6073 (tmm-80) REVERT: A 255 ARG cc_start: 0.6871 (ttt-90) cc_final: 0.6579 (tpt-90) REVERT: A 318 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 484 TYR cc_start: 0.6988 (t80) cc_final: 0.6643 (t80) REVERT: A 485 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: A 654 LYS cc_start: 0.7381 (tptt) cc_final: 0.6689 (mttt) REVERT: A 665 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7516 (mt) outliers start: 16 outliers final: 5 residues processed: 70 average time/residue: 0.6135 time to fit residues: 45.1866 Evaluate side-chains 63 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.188090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142498 restraints weight = 7654.806| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.28 r_work: 0.3364 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6919 Z= 0.143 Angle : 0.546 6.948 9541 Z= 0.293 Chirality : 0.042 0.171 1067 Planarity : 0.005 0.042 1133 Dihedral : 14.835 139.569 1256 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.02 % Allowed : 11.82 % Favored : 86.16 % 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: 0.50 (0.31), residues: 754 helix: 1.57 (0.35), residues: 224 sheet: -0.01 (0.40), residues: 188 loop : -0.21 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 490 TYR 0.012 0.001 TYR A 143 PHE 0.012 0.001 PHE A 232 TRP 0.012 0.001 TRP A 570 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6919) covalent geometry : angle 0.54584 / 0.29 ( 9541) hydrogen bonds : bond 0.03991 / 2.72 ( 260) hydrogen bonds : angle 5.04535 / 3.69 ( 736) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.244 Fit side-chains REVERT: A 27 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.5977 (tmm-80) REVERT: A 255 ARG cc_start: 0.6821 (ttt-90) cc_final: 0.6509 (tpt-90) REVERT: A 318 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: A 484 TYR cc_start: 0.6836 (t80) cc_final: 0.6578 (t80) REVERT: A 485 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: A 654 LYS cc_start: 0.7308 (tptt) cc_final: 0.6620 (mttt) REVERT: A 665 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7474 (mt) outliers start: 13 outliers final: 3 residues processed: 64 average time/residue: 0.6346 time to fit residues: 42.6308 Evaluate side-chains 62 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.189793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146461 restraints weight = 7653.944| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.10 r_work: 0.3420 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6919 Z= 0.166 Angle : 0.566 6.916 9541 Z= 0.301 Chirality : 0.043 0.178 1067 Planarity : 0.005 0.040 1133 Dihedral : 14.883 139.869 1256 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.33 % Allowed : 12.75 % Favored : 84.91 % 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: 0.49 (0.31), residues: 754 helix: 1.54 (0.35), residues: 225 sheet: -0.06 (0.39), residues: 196 loop : -0.17 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.013 0.002 TYR A 143 PHE 0.013 0.001 PHE A 232 TRP 0.012 0.002 TRP A 136 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 6919) covalent geometry : angle 0.56608 / 0.30 ( 9541) hydrogen bonds : bond 0.04205 / 2.85 ( 260) hydrogen bonds : angle 4.98458 / 3.63 ( 736) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.225 Fit side-chains REVERT: A 27 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6124 (tmm-80) REVERT: A 189 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7445 (m90) REVERT: A 255 ARG cc_start: 0.7039 (ttt-90) cc_final: 0.6634 (tpt-90) REVERT: A 318 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: A 484 TYR cc_start: 0.6936 (t80) cc_final: 0.6670 (t80) REVERT: A 485 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: A 654 LYS cc_start: 0.7392 (tptt) cc_final: 0.6727 (mttt) REVERT: A 665 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 674 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8783 (t0) REVERT: A 758 ARG cc_start: 0.6714 (mmm160) cc_final: 0.5666 (mmt90) outliers start: 15 outliers final: 3 residues processed: 67 average time/residue: 0.6826 time to fit residues: 47.9535 Evaluate side-chains 62 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 674 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.191647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.147532 restraints weight = 7649.393| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.03 r_work: 0.3429 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6919 Z= 0.127 Angle : 0.521 6.951 9541 Z= 0.280 Chirality : 0.041 0.167 1067 Planarity : 0.005 0.071 1133 Dihedral : 14.827 139.955 1256 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.56 % Allowed : 14.62 % Favored : 83.83 % 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: 0.59 (0.31), residues: 754 helix: 1.70 (0.35), residues: 225 sheet: -0.06 (0.39), residues: 196 loop : -0.13 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.012 0.001 TYR A 380 PHE 0.011 0.001 PHE A 232 TRP 0.012 0.001 TRP A 136 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6919) covalent geometry : angle 0.52122 / 0.28 ( 9541) hydrogen bonds : bond 0.03715 / 2.51 ( 260) hydrogen bonds : angle 4.85315 / 3.55 ( 736) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.252 Fit side-chains REVERT: A 189 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.7394 (m90) REVERT: A 193 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 255 ARG cc_start: 0.7045 (ttt-90) cc_final: 0.6640 (tpt-90) REVERT: A 318 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: A 387 MET cc_start: 0.8087 (mmp) cc_final: 0.7807 (mmm) REVERT: A 484 TYR cc_start: 0.6955 (t80) cc_final: 0.6681 (t80) REVERT: A 654 LYS cc_start: 0.7359 (tptt) cc_final: 0.6646 (mttt) REVERT: A 665 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7507 (mt) REVERT: A 758 ARG cc_start: 0.6732 (mmm160) cc_final: 0.5689 (mmt90) outliers start: 10 outliers final: 1 residues processed: 64 average time/residue: 0.6993 time to fit residues: 46.8444 Evaluate side-chains 64 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 44 optimal weight: 0.0570 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.193068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148295 restraints weight = 7601.397| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.96 r_work: 0.3427 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6919 Z= 0.133 Angle : 0.527 6.920 9541 Z= 0.283 Chirality : 0.041 0.169 1067 Planarity : 0.005 0.063 1133 Dihedral : 14.839 139.981 1256 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.71 % Allowed : 15.40 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.31), residues: 754 helix: 1.73 (0.35), residues: 225 sheet: -0.06 (0.39), residues: 196 loop : -0.15 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 489 TYR 0.012 0.001 TYR A 380 PHE 0.011 0.001 PHE A 232 TRP 0.018 0.001 TRP A 65 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6919) covalent geometry : angle 0.52729 / 0.28 ( 9541) hydrogen bonds : bond 0.03714 / 2.50 ( 260) hydrogen bonds : angle 4.76940 / 3.48 ( 736) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7623 (ttt90) cc_final: 0.7208 (tmm-80) REVERT: A 189 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7491 (m90) REVERT: A 193 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 255 ARG cc_start: 0.7043 (ttt-90) cc_final: 0.6607 (tpt-90) REVERT: A 318 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: A 387 MET cc_start: 0.8144 (mmp) cc_final: 0.7890 (mmm) REVERT: A 484 TYR cc_start: 0.6977 (t80) cc_final: 0.6696 (t80) REVERT: A 489 ARG cc_start: 0.6805 (ttm-80) cc_final: 0.6303 (mpt180) REVERT: A 654 LYS cc_start: 0.7277 (tptt) cc_final: 0.6577 (mptt) REVERT: A 665 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7495 (mt) REVERT: A 758 ARG cc_start: 0.6690 (mmm160) cc_final: 0.5685 (mmt90) outliers start: 11 outliers final: 3 residues processed: 64 average time/residue: 0.6214 time to fit residues: 41.7178 Evaluate side-chains 61 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.191988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147277 restraints weight = 7666.158| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.94 r_work: 0.3426 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6919 Z= 0.128 Angle : 0.522 6.922 9541 Z= 0.282 Chirality : 0.041 0.168 1067 Planarity : 0.005 0.059 1133 Dihedral : 14.810 140.121 1256 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.40 % Allowed : 16.02 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.31), residues: 754 helix: 1.80 (0.35), residues: 225 sheet: -0.04 (0.39), residues: 196 loop : -0.18 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.012 0.001 TYR A 380 PHE 0.010 0.001 PHE A 232 TRP 0.015 0.001 TRP A 65 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6919) covalent geometry : angle 0.52232 / 0.28 ( 9541) hydrogen bonds : bond 0.03609 / 2.44 ( 260) hydrogen bonds : angle 4.72546 / 3.45 ( 736) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7633 (ttt90) cc_final: 0.7221 (tmm-80) REVERT: A 189 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7506 (m90) REVERT: A 193 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 255 ARG cc_start: 0.7081 (ttt-90) cc_final: 0.6635 (tpt-90) REVERT: A 318 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: A 387 MET cc_start: 0.8167 (mmp) cc_final: 0.7907 (mmm) REVERT: A 484 TYR cc_start: 0.6959 (t80) cc_final: 0.6692 (t80) REVERT: A 654 LYS cc_start: 0.7227 (tptt) cc_final: 0.6579 (mptt) REVERT: A 665 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 758 ARG cc_start: 0.6708 (mmm160) cc_final: 0.5738 (mmt90) outliers start: 9 outliers final: 2 residues processed: 63 average time/residue: 0.6083 time to fit residues: 40.1784 Evaluate side-chains 63 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.192239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148562 restraints weight = 7653.553| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.08 r_work: 0.3447 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6919 Z= 0.125 Angle : 0.518 6.902 9541 Z= 0.279 Chirality : 0.041 0.168 1067 Planarity : 0.005 0.057 1133 Dihedral : 14.744 140.223 1256 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.09 % Allowed : 16.33 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.31), residues: 754 helix: 1.84 (0.35), residues: 225 sheet: -0.01 (0.39), residues: 196 loop : -0.20 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.012 0.001 TYR A 380 PHE 0.010 0.001 PHE A 232 TRP 0.015 0.001 TRP A 65 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6919) covalent geometry : angle 0.51814 / 0.28 ( 9541) hydrogen bonds : bond 0.03530 / 2.38 ( 260) hydrogen bonds : angle 4.67611 / 3.42 ( 736) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7631 (ttt90) cc_final: 0.7210 (tmm-80) REVERT: A 189 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7527 (m90) REVERT: A 255 ARG cc_start: 0.7069 (ttt-90) cc_final: 0.6635 (tpt-90) REVERT: A 318 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: A 387 MET cc_start: 0.8176 (mmp) cc_final: 0.7939 (mmm) REVERT: A 484 TYR cc_start: 0.6981 (t80) cc_final: 0.6690 (t80) REVERT: A 654 LYS cc_start: 0.7244 (tptt) cc_final: 0.6601 (mptt) REVERT: A 665 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7367 (mt) REVERT: A 758 ARG cc_start: 0.6708 (mmm160) cc_final: 0.5701 (mmt90) outliers start: 7 outliers final: 2 residues processed: 64 average time/residue: 0.5207 time to fit residues: 34.9697 Evaluate side-chains 58 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.192589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148993 restraints weight = 7710.398| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.07 r_work: 0.3461 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6919 Z= 0.112 Angle : 0.516 7.125 9541 Z= 0.277 Chirality : 0.040 0.165 1067 Planarity : 0.005 0.056 1133 Dihedral : 14.680 140.201 1256 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.93 % Allowed : 16.95 % Favored : 82.12 % 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: 0.72 (0.31), residues: 754 helix: 1.91 (0.35), residues: 225 sheet: 0.10 (0.39), residues: 197 loop : -0.20 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 489 TYR 0.012 0.001 TYR A 380 PHE 0.010 0.001 PHE A 219 TRP 0.017 0.001 TRP A 136 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6919) covalent geometry : angle 0.51572 / 0.28 ( 9541) hydrogen bonds : bond 0.03363 / 2.25 ( 260) hydrogen bonds : angle 4.66079 / 3.42 ( 736) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7191 (tmm-80) REVERT: A 255 ARG cc_start: 0.7060 (ttt-90) cc_final: 0.6631 (tpt-90) REVERT: A 318 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: A 387 MET cc_start: 0.8157 (mmp) cc_final: 0.7937 (mmm) REVERT: A 484 TYR cc_start: 0.6980 (t80) cc_final: 0.6665 (t80) REVERT: A 573 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7528 (tpt-90) REVERT: A 654 LYS cc_start: 0.7226 (tptt) cc_final: 0.6593 (mptt) REVERT: A 758 ARG cc_start: 0.6707 (mmm160) cc_final: 0.5703 (mmt90) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.5467 time to fit residues: 34.3378 Evaluate side-chains 58 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 318 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.192180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148984 restraints weight = 7661.397| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.06 r_work: 0.3434 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6919 Z= 0.112 Angle : 0.514 6.934 9541 Z= 0.276 Chirality : 0.040 0.164 1067 Planarity : 0.005 0.055 1133 Dihedral : 14.640 140.264 1256 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.62 % Allowed : 17.26 % Favored : 82.12 % 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: 0.76 (0.31), residues: 754 helix: 1.98 (0.35), residues: 225 sheet: 0.13 (0.39), residues: 197 loop : -0.22 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 489 TYR 0.012 0.001 TYR A 380 PHE 0.008 0.001 PHE A 232 TRP 0.013 0.001 TRP A 65 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6919) covalent geometry : angle 0.51368 / 0.28 ( 9541) hydrogen bonds : bond 0.03310 / 2.22 ( 260) hydrogen bonds : angle 4.59778 / 3.37 ( 736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.47 seconds wall clock time: 39 minutes 44.72 seconds (2384.72 seconds total)