Starting phenix.real_space_refine on Tue Feb 11 17:29:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7to2_26027/02_2025/7to2_26027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to2_26027/02_2025/7to2_26027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7to2_26027/02_2025/7to2_26027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to2_26027/02_2025/7to2_26027.map" model { file = "/net/cci-nas-00/data/ceres_data/7to2_26027/02_2025/7to2_26027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to2_26027/02_2025/7to2_26027.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3733 2.51 5 N 1039 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5384 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 25, 'TRANS': 644} Chain breaks: 1 Chain: "B" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 639 Classifications: {'RNA': 30} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 15} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 40.487 21.767 28.769 1.00 38.49 S ATOM 4596 SG CYS A 813 39.020 18.506 27.949 1.00 48.41 S ATOM 4908 SG CYS A 864 40.109 19.526 24.622 1.00 65.65 S ATOM 4947 SG CYS A 869 37.263 21.217 26.585 1.00 66.55 S Time building chain proxies: 4.05, per 1000 atoms: 0.67 Number of scatterers: 6052 At special positions: 0 Unit cell: (87.15, 97.65, 72.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 32 15.00 Mg 1 11.99 O 1213 8.00 N 1039 7.00 C 3733 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: 1.55 Conformation dependent library (CDL) restraints added in 808.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " Number of angles added : 6 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 48.8% alpha, 8.8% beta 15 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.621A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.572A pdb=" N VAL A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.656A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.567A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.833A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.851A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.609A pdb=" N LEU A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.519A pdb=" N MET A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 556 Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.609A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.935A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 746 through 769 Processing helix chain 'A' and resid 772 through 792 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.524A pdb=" N LYS A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 840' Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323 removed outlier: 6.958A pdb=" N THR A 322 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 293 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 346 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N PHE A 295 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET A 369 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 removed outlier: 6.372A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR A 742 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 461 " --> pdb=" O THR A 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.336A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.226A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 833 removed outlier: 4.455A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 844 removed outlier: 3.968A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.79 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: 1473 1.33 - 1.45: 1254 1.45 - 1.57: 3397 1.57 - 1.70: 61 1.70 - 1.82: 46 Bond restraints: 6231 Sorted by residual: bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.394 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.25e+01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.61e+00 bond pdb=" N VAL A 800 " pdb=" CA VAL A 800 " ideal model delta sigma weight residual 1.457 1.485 -0.028 9.00e-03 1.23e+04 9.47e+00 bond pdb=" N VAL A 699 " pdb=" CA VAL A 699 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.18e-02 7.18e+03 9.11e+00 ... (remaining 6226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 7524 1.82 - 3.64: 1000 3.64 - 5.46: 18 5.46 - 7.27: 6 7.27 - 9.09: 2 Bond angle restraints: 8550 Sorted by residual: angle pdb=" C PRO A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta sigma weight residual 121.65 124.64 -2.99 6.80e-01 2.16e+00 1.93e+01 angle pdb=" C2' U B 8 " pdb=" C1' U B 8 " pdb=" N1 U B 8 " ideal model delta sigma weight residual 112.00 116.55 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" N1 ADP A1003 " pdb=" C2 ADP A1003 " pdb=" N3 ADP A1003 " ideal model delta sigma weight residual 120.00 129.09 -9.09 3.00e+00 1.11e-01 9.19e+00 angle pdb=" N ILE A 467 " pdb=" CA ILE A 467 " pdb=" C ILE A 467 " ideal model delta sigma weight residual 111.90 109.57 2.33 8.10e-01 1.52e+00 8.27e+00 angle pdb=" CA LYS A 528 " pdb=" C LYS A 528 " pdb=" O LYS A 528 " ideal model delta sigma weight residual 120.70 117.78 2.92 1.03e+00 9.43e-01 8.03e+00 ... (remaining 8545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3421 16.18 - 32.37: 275 32.37 - 48.55: 77 48.55 - 64.73: 51 64.73 - 80.91: 19 Dihedral angle restraints: 3843 sinusoidal: 1878 harmonic: 1965 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 -7.40 -52.60 1 2.00e+01 2.50e-03 9.42e+00 dihedral pdb=" CA LEU A 430 " pdb=" CB LEU A 430 " pdb=" CG LEU A 430 " pdb=" CD1 LEU A 430 " ideal model delta sinusoidal sigma weight residual 180.00 124.30 55.70 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CA ASP A 562 " pdb=" CB ASP A 562 " pdb=" CG ASP A 562 " pdb=" OD1 ASP A 562 " ideal model delta sinusoidal sigma weight residual -30.00 -81.64 51.64 1 2.00e+01 2.50e-03 9.11e+00 ... (remaining 3840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 427 0.043 - 0.085: 294 0.085 - 0.128: 224 0.128 - 0.171: 32 0.171 - 0.213: 2 Chirality restraints: 979 Sorted by residual: chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 631 " pdb=" CA ILE A 631 " pdb=" CG1 ILE A 631 " pdb=" CG2 ILE A 631 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" P G B 45 " pdb=" OP1 G B 45 " pdb=" OP2 G B 45 " pdb=" O5' G B 45 " both_signs ideal model delta sigma weight residual True 2.41 -2.25 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 976 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 10 " -0.026 2.00e-02 2.50e+03 9.93e-03 2.96e+00 pdb=" N9 G B 10 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G B 10 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G B 10 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 10 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 10 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 10 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 10 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 490 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C CYS A 490 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS A 490 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 491 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1003 " 0.011 2.00e-02 2.50e+03 9.35e-03 2.40e+00 pdb=" C2 ADP A1003 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP A1003 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" C6 ADP A1003 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ADP A1003 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP A1003 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N6 ADP A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N7 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" N9 ADP A1003 " -0.013 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1185 2.81 - 3.33: 5962 3.33 - 3.85: 10226 3.85 - 4.38: 11711 4.38 - 4.90: 19769 Nonbonded interactions: 48853 Sorted by model distance: nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.284 3.120 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.296 3.040 nonbonded pdb=" O THR A 662 " pdb=" NE2 GLN A 678 " model vdw 2.334 3.120 nonbonded pdb=" O ASP A 690 " pdb=" ND1 HIS A 691 " model vdw 2.348 3.120 nonbonded pdb=" O SER A 698 " pdb=" OG SER A 698 " model vdw 2.353 3.040 ... (remaining 48848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.011 0.096 6231 Z= 0.693 Angle : 1.131 9.092 8550 Z= 0.827 Chirality : 0.069 0.213 979 Planarity : 0.004 0.016 979 Dihedral : 15.499 80.913 2567 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.84 % Allowed : 6.86 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.30), residues: 666 helix: 0.75 (0.28), residues: 298 sheet: -3.26 (0.49), residues: 75 loop : -3.04 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 771 HIS 0.005 0.001 HIS A 782 PHE 0.011 0.003 PHE A 460 TYR 0.012 0.003 TYR A 548 ARG 0.008 0.001 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.516 Fit side-chains REVERT: A 457 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7624 (tp-100) outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 0.2007 time to fit residues: 24.4404 Evaluate side-chains 60 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 775 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 375 HIS ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN A 500 GLN A 769 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095890 restraints weight = 8164.842| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.29 r_work: 0.3021 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6231 Z= 0.156 Angle : 0.492 6.511 8550 Z= 0.241 Chirality : 0.038 0.136 979 Planarity : 0.003 0.025 979 Dihedral : 15.053 80.921 1203 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.67 % Allowed : 12.37 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.32), residues: 666 helix: 1.77 (0.29), residues: 309 sheet: -2.99 (0.51), residues: 76 loop : -2.79 (0.30), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.002 0.000 HIS A 876 PHE 0.005 0.001 PHE A 918 TYR 0.007 0.001 TYR A 246 ARG 0.004 0.000 ARG A 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.610 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.1534 time to fit residues: 16.2331 Evaluate side-chains 61 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 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 = 0.3421 r_free = 0.3421 target = 0.117139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095239 restraints weight = 8257.905| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.35 r_work: 0.2997 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6231 Z= 0.160 Angle : 0.478 5.734 8550 Z= 0.234 Chirality : 0.038 0.133 979 Planarity : 0.003 0.027 979 Dihedral : 15.009 83.210 1199 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.01 % Allowed : 14.21 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.32), residues: 666 helix: 2.20 (0.29), residues: 305 sheet: -2.72 (0.52), residues: 76 loop : -2.48 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 876 PHE 0.006 0.001 PHE A 371 TYR 0.009 0.001 TYR A 473 ARG 0.002 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.625 Fit side-chains REVERT: A 592 GLU cc_start: 0.8361 (tp30) cc_final: 0.8103 (tm-30) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.1473 time to fit residues: 15.5520 Evaluate side-chains 64 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.0270 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094556 restraints weight = 8309.523| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.31 r_work: 0.3013 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6231 Z= 0.152 Angle : 0.471 5.737 8550 Z= 0.230 Chirality : 0.038 0.140 979 Planarity : 0.003 0.028 979 Dihedral : 14.976 84.868 1197 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.67 % Allowed : 15.72 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.33), residues: 666 helix: 2.41 (0.29), residues: 305 sheet: -2.48 (0.54), residues: 76 loop : -2.34 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 PHE 0.006 0.001 PHE A 371 TYR 0.012 0.001 TYR A 473 ARG 0.002 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 592 GLU cc_start: 0.8276 (tp30) cc_final: 0.8075 (tm-30) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.1495 time to fit residues: 15.4538 Evaluate side-chains 66 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.093736 restraints weight = 8385.332| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.32 r_work: 0.2958 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.213 Angle : 0.503 5.708 8550 Z= 0.248 Chirality : 0.038 0.136 979 Planarity : 0.003 0.029 979 Dihedral : 14.989 85.507 1197 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.17 % Allowed : 16.56 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.33), residues: 666 helix: 2.47 (0.29), residues: 305 sheet: -2.32 (0.61), residues: 64 loop : -2.17 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.001 HIS A 280 PHE 0.007 0.001 PHE A 295 TYR 0.014 0.001 TYR A 473 ARG 0.006 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.520 Fit side-chains REVERT: A 339 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8227 (tm-30) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 0.1271 time to fit residues: 12.8288 Evaluate side-chains 67 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 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 = 0.3326 r_free = 0.3326 target = 0.109911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087750 restraints weight = 8318.473| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.32 r_work: 0.2889 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6231 Z= 0.354 Angle : 0.566 5.718 8550 Z= 0.282 Chirality : 0.041 0.150 979 Planarity : 0.003 0.031 979 Dihedral : 15.020 85.084 1197 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.84 % Allowed : 16.89 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.33), residues: 666 helix: 2.24 (0.29), residues: 310 sheet: -2.31 (0.56), residues: 72 loop : -2.21 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 646 HIS 0.003 0.001 HIS A 280 PHE 0.009 0.001 PHE A 295 TYR 0.012 0.001 TYR A 473 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.727 Fit side-chains REVERT: A 339 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8229 (tm-30) REVERT: A 834 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8399 (tp) outliers start: 17 outliers final: 10 residues processed: 65 average time/residue: 0.1441 time to fit residues: 13.7407 Evaluate side-chains 61 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 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 = 0.3358 r_free = 0.3358 target = 0.112191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090077 restraints weight = 8316.610| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.34 r_work: 0.2913 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 0.028 6231 Z= 0.225 Angle : 0.521 8.009 8550 Z= 0.257 Chirality : 0.039 0.136 979 Planarity : 0.003 0.033 979 Dihedral : 15.012 85.858 1197 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.17 % Allowed : 17.89 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.33), residues: 666 helix: 2.24 (0.29), residues: 316 sheet: -2.20 (0.63), residues: 64 loop : -2.20 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 512 HIS 0.002 0.000 HIS A 280 PHE 0.005 0.001 PHE A 295 TYR 0.008 0.001 TYR A 473 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.748 Fit side-chains REVERT: A 339 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8216 (tm-30) REVERT: A 878 LYS cc_start: 0.8185 (tmtt) cc_final: 0.7311 (tmtt) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.1382 time to fit residues: 12.9436 Evaluate side-chains 57 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.0050 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 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 = 0.3416 r_free = 0.3416 target = 0.116760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095564 restraints weight = 8245.123| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.28 r_work: 0.2984 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6231 Z= 0.152 Angle : 0.491 6.669 8550 Z= 0.244 Chirality : 0.038 0.149 979 Planarity : 0.003 0.034 979 Dihedral : 15.051 87.183 1197 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.51 % Allowed : 17.39 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.33), residues: 666 helix: 2.57 (0.29), residues: 306 sheet: -2.06 (0.64), residues: 64 loop : -1.99 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 512 HIS 0.001 0.000 HIS A 280 PHE 0.005 0.001 PHE A 371 TYR 0.012 0.001 TYR A 473 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.539 Fit side-chains REVERT: A 339 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8173 (tm-30) REVERT: A 878 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7021 (tmtt) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.1434 time to fit residues: 12.8562 Evaluate side-chains 60 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 22 optimal weight: 0.0070 chunk 8 optimal weight: 5.9990 chunk 58 optimal weight: 0.0020 chunk 64 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 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 = 0.3421 r_free = 0.3421 target = 0.116611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095271 restraints weight = 8217.168| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.30 r_work: 0.3012 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6231 Z= 0.138 Angle : 0.497 8.492 8550 Z= 0.246 Chirality : 0.038 0.141 979 Planarity : 0.003 0.033 979 Dihedral : 15.079 87.547 1197 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.34 % Allowed : 17.73 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.33), residues: 666 helix: 2.68 (0.29), residues: 306 sheet: -1.79 (0.66), residues: 64 loop : -1.94 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 512 HIS 0.001 0.000 HIS A 280 PHE 0.004 0.001 PHE A 371 TYR 0.015 0.001 TYR A 473 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.640 Fit side-chains REVERT: A 339 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8265 (tm-30) REVERT: A 834 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 878 LYS cc_start: 0.7742 (tmtt) cc_final: 0.7024 (tmtt) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.1571 time to fit residues: 14.9605 Evaluate side-chains 63 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 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 = 0.3407 r_free = 0.3407 target = 0.115851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094106 restraints weight = 8273.340| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.31 r_work: 0.2991 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6231 Z= 0.170 Angle : 0.512 8.584 8550 Z= 0.253 Chirality : 0.038 0.146 979 Planarity : 0.003 0.035 979 Dihedral : 15.056 87.239 1197 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.34 % Allowed : 17.39 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.33), residues: 666 helix: 2.74 (0.29), residues: 306 sheet: -1.67 (0.67), residues: 64 loop : -1.91 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 PHE 0.005 0.001 PHE A 371 TYR 0.018 0.001 TYR A 473 ARG 0.006 0.000 ARG A 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.618 Fit side-chains REVERT: A 339 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8275 (tm-30) REVERT: A 834 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8382 (tp) REVERT: A 878 LYS cc_start: 0.7814 (tmtt) cc_final: 0.7044 (tmtt) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1404 time to fit residues: 12.9823 Evaluate side-chains 62 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 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 = 0.3403 r_free = 0.3403 target = 0.115596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093580 restraints weight = 8479.661| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.36 r_work: 0.2978 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6231 Z= 0.169 Angle : 0.498 8.661 8550 Z= 0.244 Chirality : 0.038 0.141 979 Planarity : 0.003 0.032 979 Dihedral : 15.059 87.284 1197 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.34 % Allowed : 17.39 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.34), residues: 666 helix: 2.76 (0.29), residues: 306 sheet: -1.64 (0.67), residues: 64 loop : -1.91 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 771 HIS 0.002 0.000 HIS A 280 PHE 0.006 0.001 PHE A 371 TYR 0.015 0.001 TYR A 473 ARG 0.006 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2902.73 seconds wall clock time: 52 minutes 21.60 seconds (3141.60 seconds total)