Starting phenix.real_space_refine on Wed Mar 4 05:27:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vbl_64926/03_2026/9vbl_64926.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vbl_64926/03_2026/9vbl_64926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vbl_64926/03_2026/9vbl_64926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vbl_64926/03_2026/9vbl_64926.map" model { file = "/net/cci-nas-00/data/ceres_data/9vbl_64926/03_2026/9vbl_64926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vbl_64926/03_2026/9vbl_64926.cif" } resolution = 3.39 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6052 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 26 5.16 5 C 3869 2.51 5 N 1000 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6052 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 20, 'TRANS': 730} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.44, per 1000 atoms: 0.24 Number of scatterers: 6052 At special positions: 0 Unit cell: (75.53, 81.34, 92.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1 15.00 O 1156 8.00 N 1000 7.00 C 3869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 188.7 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 52.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.550A pdb=" N SER A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.724A pdb=" N ASN A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 removed outlier: 3.969A pdb=" N LEU A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.994A pdb=" N GLU A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.756A pdb=" N LYS A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.998A pdb=" N VAL A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 removed outlier: 4.162A pdb=" N ARG A 437 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.999A pdb=" N GLU A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 448 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.558A pdb=" N GLN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 504 through 517 removed outlier: 3.908A pdb=" N TYR A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.810A pdb=" N ILE A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.803A pdb=" N LYS A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 600 through 608 removed outlier: 4.006A pdb=" N LLP A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN A 608 " --> pdb=" O LLP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 628 removed outlier: 4.510A pdb=" N GLU A 622 " --> pdb=" O GLY A 618 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.562A pdb=" N TYR A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 668 removed outlier: 3.596A pdb=" N VAL A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.894A pdb=" N ILE A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 717 removed outlier: 3.727A pdb=" N TYR A 706 " --> pdb=" O ASP A 702 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 removed outlier: 3.732A pdb=" N LYS A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.620A pdb=" N THR A 158 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.620A pdb=" N THR A 158 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY A 122 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS A 191 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 125 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS A 49 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA5, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AA6, first strand: chain 'A' and resid 564 through 568 removed outlier: 6.914A pdb=" N PHE A 488 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU A 588 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 490 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER A 587 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 612 " --> pdb=" O TYR A 633 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1948 1.34 - 1.46: 844 1.46 - 1.57: 3333 1.57 - 1.69: 1 1.69 - 1.81: 45 Bond restraints: 6171 Sorted by residual: bond pdb=" OP4 LLP A 604 " pdb=" P LLP A 604 " ideal model delta sigma weight residual 1.726 1.543 0.183 2.00e-02 2.50e+03 8.33e+01 bond pdb=" NZ LLP A 604 " pdb=" C4' LLP A 604 " ideal model delta sigma weight residual 1.273 1.430 -0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" C4 LLP A 604 " pdb=" C4' LLP A 604 " ideal model delta sigma weight residual 1.464 1.613 -0.149 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C6 LLP A 604 " pdb=" N1 LLP A 604 " ideal model delta sigma weight residual 1.333 1.402 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C3 LLP A 604 " pdb=" O3 LLP A 604 " ideal model delta sigma weight residual 1.330 1.397 -0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 6166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 8224 2.33 - 4.66: 111 4.66 - 6.99: 11 6.99 - 9.32: 2 9.32 - 11.65: 1 Bond angle restraints: 8349 Sorted by residual: angle pdb=" CE LLP A 604 " pdb=" NZ LLP A 604 " pdb=" C4' LLP A 604 " ideal model delta sigma weight residual 119.26 107.61 11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C ILE A 581 " pdb=" CA ILE A 581 " pdb=" CB ILE A 581 " ideal model delta sigma weight residual 113.70 110.35 3.35 9.50e-01 1.11e+00 1.25e+01 angle pdb=" OP1 LLP A 604 " pdb=" P LLP A 604 " pdb=" OP4 LLP A 604 " ideal model delta sigma weight residual 100.47 109.70 -9.23 3.00e+00 1.11e-01 9.47e+00 angle pdb=" N VAL A 433 " pdb=" CA VAL A 433 " pdb=" C VAL A 433 " ideal model delta sigma weight residual 106.21 109.49 -3.28 1.07e+00 8.73e-01 9.42e+00 angle pdb=" NZ LLP A 604 " pdb=" C4' LLP A 604 " pdb=" C4 LLP A 604 " ideal model delta sigma weight residual 120.09 111.93 8.16 3.00e+00 1.11e-01 7.40e+00 ... (remaining 8344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3332 17.31 - 34.61: 304 34.61 - 51.92: 51 51.92 - 69.23: 27 69.23 - 86.53: 3 Dihedral angle restraints: 3717 sinusoidal: 1515 harmonic: 2202 Sorted by residual: dihedral pdb=" CA VAL A 611 " pdb=" C VAL A 611 " pdb=" N THR A 612 " pdb=" CA THR A 612 " ideal model delta harmonic sigma weight residual 180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLU A 622 " pdb=" C GLU A 622 " pdb=" N ILE A 623 " pdb=" CA ILE A 623 " ideal model delta harmonic sigma weight residual 180.00 164.54 15.46 0 5.00e+00 4.00e-02 9.56e+00 dihedral pdb=" CB MET A 336 " pdb=" CG MET A 336 " pdb=" SD MET A 336 " pdb=" CE MET A 336 " ideal model delta sinusoidal sigma weight residual 60.00 117.36 -57.36 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 536 0.035 - 0.070: 307 0.070 - 0.105: 70 0.105 - 0.140: 12 0.140 - 0.175: 2 Chirality restraints: 927 Sorted by residual: chirality pdb=" CA GLN A 625 " pdb=" N GLN A 625 " pdb=" C GLN A 625 " pdb=" CB GLN A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CA GLN A 241 " pdb=" N GLN A 241 " pdb=" C GLN A 241 " pdb=" CB GLN A 241 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CG LEU A 495 " pdb=" CB LEU A 495 " pdb=" CD1 LEU A 495 " pdb=" CD2 LEU A 495 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 924 not shown) Planarity restraints: 1073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 604 " -0.211 2.00e-02 2.50e+03 2.04e-01 4.16e+02 pdb=" NZ LLP A 604 " 0.191 2.00e-02 2.50e+03 pdb=" C4 LLP A 604 " -0.197 2.00e-02 2.50e+03 pdb=" C4' LLP A 604 " 0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 400 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 401 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 401 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 401 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 621 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C VAL A 621 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 621 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 622 " -0.011 2.00e-02 2.50e+03 ... (remaining 1070 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 198 2.71 - 3.26: 5953 3.26 - 3.80: 9359 3.80 - 4.35: 12723 4.35 - 4.90: 21275 Nonbonded interactions: 49508 Sorted by model distance: nonbonded pdb=" OE2 GLU A 497 " pdb=" OH TYR A 537 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASN A 504 " pdb=" OH TYR A 706 " model vdw 2.189 3.040 nonbonded pdb=" O ILE A 303 " pdb=" OG1 THR A 307 " model vdw 2.193 3.040 nonbonded pdb=" OE2 GLU A 588 " pdb=" OH TYR A 706 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASP A 230 " pdb=" N LYS A 231 " model vdw 2.264 3.120 ... (remaining 49503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 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 : 0.006 0.183 6171 Z= 0.276 Angle : 0.751 11.647 8349 Z= 0.457 Chirality : 0.043 0.175 927 Planarity : 0.007 0.204 1073 Dihedral : 14.545 86.533 2299 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.19 (0.30), residues: 746 helix: -1.09 (0.27), residues: 374 sheet: -2.19 (0.50), residues: 110 loop : -1.34 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 437 TYR 0.019 0.002 TYR A 239 PHE 0.026 0.002 PHE A 243 TRP 0.011 0.001 TRP A 416 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 6171) covalent geometry : angle 0.75064 ( 8349) hydrogen bonds : bond 0.22310 ( 256) hydrogen bonds : angle 7.71740 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 421 ASP cc_start: 0.5340 (t0) cc_final: 0.5103 (t0) REVERT: A 596 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6782 (mt-10) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0595 time to fit residues: 7.4519 Evaluate side-chains 63 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.144669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123153 restraints weight = 7411.082| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.15 r_work: 0.3524 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6171 Z= 0.138 Angle : 0.561 6.928 8349 Z= 0.295 Chirality : 0.042 0.136 927 Planarity : 0.004 0.039 1073 Dihedral : 5.832 71.412 815 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.22 % Allowed : 7.49 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.32), residues: 746 helix: -0.43 (0.27), residues: 370 sheet: -1.80 (0.52), residues: 112 loop : -0.83 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.017 0.002 TYR A 185 PHE 0.013 0.002 PHE A 605 TRP 0.013 0.001 TRP A 427 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6171) covalent geometry : angle 0.56094 ( 8349) hydrogen bonds : bond 0.04235 ( 256) hydrogen bonds : angle 4.90974 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 241 GLN cc_start: 0.6603 (mp10) cc_final: 0.6351 (mp10) REVERT: A 427 TRP cc_start: 0.6777 (t60) cc_final: 0.6491 (t60) REVERT: A 527 MET cc_start: 0.5603 (ptp) cc_final: 0.5258 (ptp) REVERT: A 581 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.6719 (mt) REVERT: A 727 MET cc_start: 0.6165 (mtt) cc_final: 0.5843 (mtm) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.0590 time to fit residues: 6.3904 Evaluate side-chains 72 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 721 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.0020 chunk 47 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.147325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125960 restraints weight = 7234.625| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.08 r_work: 0.3575 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6171 Z= 0.097 Angle : 0.492 7.940 8349 Z= 0.257 Chirality : 0.040 0.134 927 Planarity : 0.003 0.034 1073 Dihedral : 5.297 61.923 815 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.68 % Allowed : 9.63 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.32), residues: 746 helix: 0.08 (0.28), residues: 370 sheet: -1.45 (0.54), residues: 112 loop : -0.63 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.016 0.001 TYR A 242 PHE 0.013 0.001 PHE A 211 TRP 0.012 0.001 TRP A 427 HIS 0.002 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6171) covalent geometry : angle 0.49163 ( 8349) hydrogen bonds : bond 0.03389 ( 256) hydrogen bonds : angle 4.44164 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 241 GLN cc_start: 0.6777 (mp10) cc_final: 0.6492 (mp10) REVERT: A 427 TRP cc_start: 0.6760 (t60) cc_final: 0.6453 (t60) REVERT: A 473 TYR cc_start: 0.7906 (t80) cc_final: 0.7658 (t80) REVERT: A 488 PHE cc_start: 0.6382 (m-10) cc_final: 0.6028 (m-80) REVERT: A 581 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6553 (mt) REVERT: A 625 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: A 727 MET cc_start: 0.5961 (mtt) cc_final: 0.5683 (mtm) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 0.0585 time to fit residues: 7.3439 Evaluate side-chains 73 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 728 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.0010 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.124111 restraints weight = 7376.860| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.14 r_work: 0.3544 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6171 Z= 0.116 Angle : 0.501 7.918 8349 Z= 0.263 Chirality : 0.041 0.138 927 Planarity : 0.003 0.034 1073 Dihedral : 5.275 55.018 815 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.75 % Allowed : 10.55 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.32), residues: 746 helix: 0.29 (0.28), residues: 370 sheet: -0.84 (0.59), residues: 100 loop : -0.71 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.014 0.001 TYR A 746 PHE 0.013 0.001 PHE A 251 TRP 0.011 0.001 TRP A 416 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6171) covalent geometry : angle 0.50112 ( 8349) hydrogen bonds : bond 0.03254 ( 256) hydrogen bonds : angle 4.23044 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7553 (t0) cc_final: 0.7317 (t0) REVERT: A 427 TRP cc_start: 0.6718 (t60) cc_final: 0.6353 (t60) REVERT: A 581 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.6697 (mt) outliers start: 18 outliers final: 11 residues processed: 79 average time/residue: 0.0480 time to fit residues: 5.7226 Evaluate side-chains 71 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 728 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.0170 chunk 57 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 273 GLN ** 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 = 0.3907 r_free = 0.3907 target = 0.144989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123520 restraints weight = 7411.172| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.10 r_work: 0.3552 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6171 Z= 0.106 Angle : 0.475 7.077 8349 Z= 0.252 Chirality : 0.040 0.139 927 Planarity : 0.003 0.033 1073 Dihedral : 5.243 57.512 815 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.14 % Allowed : 11.16 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.32), residues: 746 helix: 0.46 (0.28), residues: 376 sheet: -0.74 (0.59), residues: 100 loop : -0.79 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.016 0.001 TYR A 473 PHE 0.023 0.002 PHE A 488 TRP 0.010 0.001 TRP A 416 HIS 0.003 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6171) covalent geometry : angle 0.47474 ( 8349) hydrogen bonds : bond 0.03105 ( 256) hydrogen bonds : angle 4.08910 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7585 (t0) cc_final: 0.7344 (t0) REVERT: A 418 MET cc_start: 0.7333 (mtt) cc_final: 0.7026 (mtm) REVERT: A 427 TRP cc_start: 0.6690 (t60) cc_final: 0.6280 (t60) REVERT: A 581 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.6684 (mt) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.0588 time to fit residues: 6.5634 Evaluate side-chains 69 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 728 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 69 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** 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 = 0.3899 r_free = 0.3899 target = 0.144349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122846 restraints weight = 7349.220| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.10 r_work: 0.3530 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6171 Z= 0.115 Angle : 0.483 6.174 8349 Z= 0.256 Chirality : 0.041 0.133 927 Planarity : 0.003 0.032 1073 Dihedral : 5.262 58.760 815 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.60 % Allowed : 10.86 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.32), residues: 746 helix: 0.55 (0.28), residues: 377 sheet: -0.70 (0.59), residues: 100 loop : -0.83 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.016 0.002 TYR A 473 PHE 0.019 0.002 PHE A 488 TRP 0.010 0.001 TRP A 416 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6171) covalent geometry : angle 0.48291 ( 8349) hydrogen bonds : bond 0.03132 ( 256) hydrogen bonds : angle 4.05781 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7609 (t0) cc_final: 0.7379 (t0) REVERT: A 259 LYS cc_start: 0.7644 (mttt) cc_final: 0.7378 (mttp) REVERT: A 418 MET cc_start: 0.7297 (mtt) cc_final: 0.7025 (mtm) REVERT: A 427 TRP cc_start: 0.6729 (t60) cc_final: 0.6282 (t60) REVERT: A 581 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.6760 (mt) outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 0.0563 time to fit residues: 6.5470 Evaluate side-chains 73 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 728 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** 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 = 0.3957 r_free = 0.3957 target = 0.148107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126435 restraints weight = 7510.851| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.14 r_work: 0.3572 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6171 Z= 0.116 Angle : 0.479 5.845 8349 Z= 0.254 Chirality : 0.041 0.136 927 Planarity : 0.003 0.031 1073 Dihedral : 5.287 59.602 815 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.99 % Allowed : 11.47 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.32), residues: 746 helix: 0.71 (0.28), residues: 372 sheet: -0.75 (0.59), residues: 100 loop : -0.78 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 345 TYR 0.015 0.001 TYR A 473 PHE 0.013 0.001 PHE A 488 TRP 0.009 0.001 TRP A 416 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6171) covalent geometry : angle 0.47852 ( 8349) hydrogen bonds : bond 0.03109 ( 256) hydrogen bonds : angle 4.06646 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7679 (t0) cc_final: 0.7451 (t0) REVERT: A 259 LYS cc_start: 0.7689 (mttt) cc_final: 0.7293 (mttp) REVERT: A 418 MET cc_start: 0.7247 (mtt) cc_final: 0.7022 (mtm) REVERT: A 581 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.6786 (mt) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.0551 time to fit residues: 6.2824 Evaluate side-chains 76 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 728 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** 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 = 0.3926 r_free = 0.3926 target = 0.145324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124452 restraints weight = 7489.271| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.04 r_work: 0.3559 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6171 Z= 0.141 Angle : 0.515 5.964 8349 Z= 0.273 Chirality : 0.041 0.138 927 Planarity : 0.003 0.035 1073 Dihedral : 5.374 59.809 815 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.14 % Allowed : 11.77 % Favored : 86.09 % 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: -0.22 (0.32), residues: 746 helix: 0.63 (0.28), residues: 373 sheet: -0.82 (0.58), residues: 100 loop : -0.82 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 41 TYR 0.016 0.002 TYR A 746 PHE 0.012 0.002 PHE A 605 TRP 0.014 0.001 TRP A 427 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6171) covalent geometry : angle 0.51485 ( 8349) hydrogen bonds : bond 0.03333 ( 256) hydrogen bonds : angle 4.12868 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7677 (t0) cc_final: 0.7452 (t0) REVERT: A 418 MET cc_start: 0.7307 (mtt) cc_final: 0.7043 (mtm) REVERT: A 581 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.6776 (mt) outliers start: 14 outliers final: 13 residues processed: 78 average time/residue: 0.0548 time to fit residues: 6.3955 Evaluate side-chains 78 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 728 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.152264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131220 restraints weight = 7509.579| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.01 r_work: 0.3651 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6171 Z= 0.124 Angle : 0.505 6.745 8349 Z= 0.268 Chirality : 0.041 0.134 927 Planarity : 0.003 0.046 1073 Dihedral : 5.335 58.886 815 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.99 % Allowed : 12.54 % Favored : 85.47 % 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: -0.20 (0.32), residues: 746 helix: 0.65 (0.28), residues: 373 sheet: -0.78 (0.58), residues: 100 loop : -0.84 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 720 TYR 0.016 0.001 TYR A 746 PHE 0.013 0.001 PHE A 251 TRP 0.020 0.001 TRP A 427 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6171) covalent geometry : angle 0.50500 ( 8349) hydrogen bonds : bond 0.03243 ( 256) hydrogen bonds : angle 4.15871 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7617 (t0) cc_final: 0.7411 (t0) REVERT: A 418 MET cc_start: 0.7272 (mtt) cc_final: 0.7049 (mtm) REVERT: A 581 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.6755 (mt) outliers start: 13 outliers final: 12 residues processed: 74 average time/residue: 0.0475 time to fit residues: 5.4654 Evaluate side-chains 76 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** 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 = 0.4004 r_free = 0.4004 target = 0.151066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130072 restraints weight = 7510.877| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.01 r_work: 0.3639 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6171 Z= 0.133 Angle : 0.520 7.221 8349 Z= 0.274 Chirality : 0.042 0.136 927 Planarity : 0.003 0.040 1073 Dihedral : 5.370 58.791 815 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.14 % Allowed : 12.08 % Favored : 85.78 % 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: -0.23 (0.32), residues: 746 helix: 0.60 (0.28), residues: 373 sheet: -0.78 (0.59), residues: 100 loop : -0.81 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 720 TYR 0.020 0.002 TYR A 185 PHE 0.011 0.002 PHE A 605 TRP 0.021 0.001 TRP A 427 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6171) covalent geometry : angle 0.51965 ( 8349) hydrogen bonds : bond 0.03316 ( 256) hydrogen bonds : angle 4.17556 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7584 (t0) cc_final: 0.7372 (t0) REVERT: A 418 MET cc_start: 0.7276 (mtt) cc_final: 0.7046 (mtm) REVERT: A 581 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.6729 (mt) REVERT: A 706 TYR cc_start: 0.6695 (t80) cc_final: 0.5661 (t80) outliers start: 14 outliers final: 13 residues processed: 77 average time/residue: 0.0498 time to fit residues: 5.9345 Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.151240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130110 restraints weight = 7461.057| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.01 r_work: 0.3636 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6171 Z= 0.137 Angle : 0.549 14.991 8349 Z= 0.283 Chirality : 0.042 0.136 927 Planarity : 0.003 0.038 1073 Dihedral : 5.403 58.638 815 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.60 % Allowed : 12.54 % Favored : 84.86 % 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: -0.25 (0.32), residues: 746 helix: 0.56 (0.28), residues: 373 sheet: -0.76 (0.59), residues: 100 loop : -0.81 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 720 TYR 0.015 0.002 TYR A 498 PHE 0.011 0.002 PHE A 605 TRP 0.020 0.001 TRP A 427 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6171) covalent geometry : angle 0.54900 ( 8349) hydrogen bonds : bond 0.03390 ( 256) hydrogen bonds : angle 4.26592 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1565.39 seconds wall clock time: 27 minutes 29.54 seconds (1649.54 seconds total)