Starting phenix.real_space_refine on Sat Jul 20 16:36:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eld_31181/07_2024/7eld_31181.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eld_31181/07_2024/7eld_31181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eld_31181/07_2024/7eld_31181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eld_31181/07_2024/7eld_31181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eld_31181/07_2024/7eld_31181.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eld_31181/07_2024/7eld_31181.cif" } resolution = 4.6 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= 0.002 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: 5 Type Number sf(0) Gaussians P 109 5.49 5 S 60 5.16 5 C 6758 2.51 5 N 1946 2.21 5 O 2409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 860": "NH1" <-> "NH2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A GLU 1209": "OE1" <-> "OE2" Residue "A ARG 1224": "NH1" <-> "NH2" Residue "A PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A TYR 1374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1628": "NH1" <-> "NH2" Residue "A GLU 1728": "OE1" <-> "OE2" Residue "A GLU 1740": "OE1" <-> "OE2" Residue "A ARG 1755": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11282 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8976 Classifications: {'peptide': 1137} Link IDs: {'PTRANS': 38, 'TRANS': 1098} Chain breaks: 12 Chain: "B" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2306 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 48, 'rna3p_pyr': 56} Link IDs: {'rna2p': 4, 'rna3p': 104} Chain breaks: 6 Time building chain proxies: 6.71, per 1000 atoms: 0.59 Number of scatterers: 11282 At special positions: 0 Unit cell: (95.316, 110.526, 188.604, 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 60 16.00 P 109 15.00 O 2409 8.00 N 1946 7.00 C 6758 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 - 3.50 Amino acid : False - 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: 4.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 57.7% alpha, 4.7% beta 43 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.523A pdb=" N ASP A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 removed outlier: 4.099A pdb=" N MET A 297 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.847A pdb=" N ASN A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 348 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.980A pdb=" N ILE A 372 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.655A pdb=" N LEU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 472 through 493 removed outlier: 3.685A pdb=" N THR A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 567 removed outlier: 6.980A pdb=" N GLN A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N TRP A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 551 " --> pdb=" O TRP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 594 removed outlier: 4.276A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 removed outlier: 3.856A pdb=" N HIS A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 673 through 687 Proline residue: A 681 - end of helix removed outlier: 3.650A pdb=" N LEU A 687 " --> pdb=" O VAL A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 721 removed outlier: 3.592A pdb=" N ASP A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 781 through 800 removed outlier: 3.905A pdb=" N PHE A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 827 through 851 removed outlier: 4.079A pdb=" N THR A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 920 Processing helix chain 'A' and resid 1049 through 1064 Processing helix chain 'A' and resid 1064 through 1069 Processing helix chain 'A' and resid 1103 through 1113 Processing helix chain 'A' and resid 1254 through 1264 Processing helix chain 'A' and resid 1301 through 1307 removed outlier: 3.580A pdb=" N VAL A1307 " --> pdb=" O LYS A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1348 Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1356 through 1364 Processing helix chain 'A' and resid 1374 through 1397 Processing helix chain 'A' and resid 1401 through 1414 Processing helix chain 'A' and resid 1414 through 1426 Processing helix chain 'A' and resid 1501 through 1517 Processing helix chain 'A' and resid 1518 through 1529 Processing helix chain 'A' and resid 1559 through 1567 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 3.707A pdb=" N LEU A1576 " --> pdb=" O GLU A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1615 removed outlier: 4.443A pdb=" N LEU A1596 " --> pdb=" O CYS A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1632 Processing helix chain 'A' and resid 1633 through 1644 Processing helix chain 'A' and resid 1645 through 1650 Processing helix chain 'A' and resid 1654 through 1668 Processing helix chain 'A' and resid 1690 through 1706 Processing helix chain 'A' and resid 1709 through 1726 removed outlier: 3.524A pdb=" N ALA A1713 " --> pdb=" O ASP A1709 " (cutoff:3.500A) Proline residue: A1719 - end of helix Proline residue: A1723 - end of helix removed outlier: 3.913A pdb=" N THR A1726 " --> pdb=" O GLN A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1742 Processing helix chain 'A' and resid 1780 through 1794 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 266 Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.623A pdb=" N GLY A 325 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 301 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 300 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 460 through 464 removed outlier: 5.453A pdb=" N ILE A 461 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 775 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 463 " --> pdb=" O VAL A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 862 through 867 Processing sheet with id=AA5, first strand: chain 'A' and resid 1036 through 1041 removed outlier: 4.343A pdb=" N PHE A1009 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A1086 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1211 through 1212 Processing sheet with id=AA7, first strand: chain 'A' and resid 1230 through 1231 Processing sheet with id=AA8, first strand: chain 'A' and resid 1760 through 1761 removed outlier: 3.683A pdb=" N ALA A1760 " --> pdb=" O GLY A1772 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1883 1.32 - 1.45: 3390 1.45 - 1.57: 6121 1.57 - 1.69: 211 1.69 - 1.81: 96 Bond restraints: 11701 Sorted by residual: bond pdb=" C VAL A 828 " pdb=" O VAL A 828 " ideal model delta sigma weight residual 1.237 1.321 -0.084 1.19e-02 7.06e+03 4.97e+01 bond pdb=" C VAL A 841 " pdb=" O VAL A 841 " ideal model delta sigma weight residual 1.237 1.306 -0.069 1.13e-02 7.83e+03 3.74e+01 bond pdb=" C ASN A 838 " pdb=" O ASN A 838 " ideal model delta sigma weight residual 1.237 1.301 -0.064 1.17e-02 7.31e+03 3.03e+01 bond pdb=" C TYR A 847 " pdb=" O TYR A 847 " ideal model delta sigma weight residual 1.237 1.298 -0.062 1.17e-02 7.31e+03 2.77e+01 bond pdb=" N VAL A 303 " pdb=" CA VAL A 303 " ideal model delta sigma weight residual 1.454 1.494 -0.040 7.70e-03 1.69e+04 2.69e+01 ... (remaining 11696 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.83: 837 106.83 - 113.75: 6618 113.75 - 120.68: 5253 120.68 - 127.61: 3387 127.61 - 134.54: 205 Bond angle restraints: 16300 Sorted by residual: angle pdb=" O3' U B 115 " pdb=" C3' U B 115 " pdb=" C2' U B 115 " ideal model delta sigma weight residual 109.50 120.57 -11.07 1.50e+00 4.44e-01 5.44e+01 angle pdb=" CA LYS A 827 " pdb=" C LYS A 827 " pdb=" N VAL A 828 " ideal model delta sigma weight residual 115.27 123.61 -8.34 1.34e+00 5.57e-01 3.87e+01 angle pdb=" O LYS A 827 " pdb=" C LYS A 827 " pdb=" N VAL A 828 " ideal model delta sigma weight residual 122.79 116.30 6.49 1.14e+00 7.69e-01 3.24e+01 angle pdb=" C ALA A 840 " pdb=" N VAL A 841 " pdb=" CA VAL A 841 " ideal model delta sigma weight residual 120.56 113.45 7.11 1.26e+00 6.30e-01 3.19e+01 angle pdb=" C HIS A 874 " pdb=" N THR A 875 " pdb=" CA THR A 875 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 ... (remaining 16295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 6723 35.28 - 70.55: 466 70.55 - 105.83: 47 105.83 - 141.10: 2 141.10 - 176.38: 1 Dihedral angle restraints: 7239 sinusoidal: 3913 harmonic: 3326 Sorted by residual: dihedral pdb=" C5' U B 115 " pdb=" C4' U B 115 " pdb=" C3' U B 115 " pdb=" O3' U B 115 " ideal model delta sinusoidal sigma weight residual 147.00 89.74 57.26 1 8.00e+00 1.56e-02 6.89e+01 dihedral pdb=" C LEU A 851 " pdb=" N LEU A 851 " pdb=" CA LEU A 851 " pdb=" CB LEU A 851 " ideal model delta harmonic sigma weight residual -122.60 -138.27 15.67 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" O4' C B 27 " pdb=" C1' C B 27 " pdb=" N1 C B 27 " pdb=" C2 C B 27 " ideal model delta sinusoidal sigma weight residual -160.00 -77.36 -82.64 1 1.50e+01 4.44e-03 3.72e+01 ... (remaining 7236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1370 0.122 - 0.245: 576 0.245 - 0.367: 11 0.367 - 0.489: 2 0.489 - 0.611: 2 Chirality restraints: 1961 Sorted by residual: chirality pdb=" C3' U B 115 " pdb=" C4' U B 115 " pdb=" O3' U B 115 " pdb=" C2' U B 115 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA LEU A 851 " pdb=" N LEU A 851 " pdb=" C LEU A 851 " pdb=" CB LEU A 851 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA ASN A1636 " pdb=" N ASN A1636 " pdb=" C ASN A1636 " pdb=" CB ASN A1636 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 1958 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 827 " 0.025 2.00e-02 2.50e+03 4.78e-02 2.29e+01 pdb=" C LYS A 827 " -0.083 2.00e-02 2.50e+03 pdb=" O LYS A 827 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL A 828 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 848 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C CYS A 848 " 0.061 2.00e-02 2.50e+03 pdb=" O CYS A 848 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A 849 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 841 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C VAL A 841 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL A 841 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY A 842 " -0.021 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4515 2.94 - 3.43: 11264 3.43 - 3.92: 21762 3.92 - 4.41: 24346 4.41 - 4.90: 33229 Nonbonded interactions: 95116 Sorted by model distance: nonbonded pdb=" O HIS A 874 " pdb=" O THR A 875 " model vdw 2.446 3.040 nonbonded pdb=" O5' G B -13 " pdb=" O4' G B -13 " model vdw 2.484 2.432 nonbonded pdb=" O GLU A 799 " pdb=" N ILE A 801 " model vdw 2.495 2.520 nonbonded pdb=" O5' A B -10 " pdb=" O4' A B -10 " model vdw 2.498 2.432 nonbonded pdb=" O5' C B 79 " pdb=" O4' C B 79 " model vdw 2.508 2.432 ... (remaining 95111 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 group one per residue 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: 0.400 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 37.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4880 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 : 0.012 0.084 11701 Z= 0.767 Angle : 1.409 11.065 16300 Z= 1.103 Chirality : 0.108 0.611 1961 Planarity : 0.005 0.059 1664 Dihedral : 20.425 176.377 5079 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.90 % Allowed : 2.88 % Favored : 96.22 % Rotamer: Outliers : 10.68 % Allowed : 12.31 % Favored : 77.01 % Cbeta Deviations : 0.56 % 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: 3.37 (0.24), residues: 1111 helix: 4.32 (0.18), residues: 605 sheet: 0.85 (0.57), residues: 83 loop : -0.80 (0.25), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 547 HIS 0.009 0.001 HIS A 387 PHE 0.010 0.001 PHE A1613 TYR 0.011 0.002 TYR A 757 ARG 0.005 0.001 ARG A1062 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 132 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7906 (p90) REVERT: A 412 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8100 (t) REVERT: A 434 LEU cc_start: 0.9705 (tp) cc_final: 0.9439 (mm) REVERT: A 474 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 552 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8801 (m) REVERT: A 556 PHE cc_start: 0.9188 (m-10) cc_final: 0.8982 (m-80) REVERT: A 794 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9125 (pt0) REVERT: A 803 ARG cc_start: 0.9618 (mtp85) cc_final: 0.9362 (mmp-170) REVERT: A 883 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7579 (mm) REVERT: A 976 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8296 (p) REVERT: A 1200 MET cc_start: 0.7283 (ttm) cc_final: 0.7065 (ttm) REVERT: A 1371 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7104 (p) REVERT: A 1416 MET cc_start: 0.8760 (mmt) cc_final: 0.8411 (mmm) REVERT: A 1497 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8946 (pt) outliers start: 105 outliers final: 25 residues processed: 222 average time/residue: 0.2872 time to fit residues: 88.2371 Evaluate side-chains 116 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 82 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 40.0000 chunk 111 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1328 GLN A1582 HIS ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1739 GLN ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11701 Z= 0.288 Angle : 0.771 9.157 16300 Z= 0.411 Chirality : 0.043 0.231 1961 Planarity : 0.005 0.053 1664 Dihedral : 21.831 179.816 2889 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 29.62 Ramachandran Plot: Outliers : 0.63 % Allowed : 2.61 % Favored : 96.76 % Rotamer: Outliers : 0.20 % Allowed : 3.97 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.24), residues: 1111 helix: 2.02 (0.19), residues: 622 sheet: -0.47 (0.50), residues: 91 loop : -1.12 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1528 HIS 0.008 0.002 HIS A1401 PHE 0.022 0.003 PHE A 785 TYR 0.036 0.002 TYR A1513 ARG 0.013 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9647 (tp) cc_final: 0.9442 (mm) REVERT: A 474 LEU cc_start: 0.9373 (mm) cc_final: 0.9158 (pp) REVERT: A 865 MET cc_start: 0.7048 (pmm) cc_final: 0.6337 (tpp) REVERT: A 1408 MET cc_start: 0.9354 (mtm) cc_final: 0.9152 (mtp) REVERT: A 1416 MET cc_start: 0.9048 (mmt) cc_final: 0.8783 (mmm) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.2753 time to fit residues: 32.4436 Evaluate side-chains 65 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 50.0000 chunk 120 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 293 GLN A 326 HIS ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A 984 HIS A1399 GLN A1606 HIS A1744 GLN ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5346 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11701 Z= 0.244 Angle : 0.708 10.740 16300 Z= 0.372 Chirality : 0.041 0.265 1961 Planarity : 0.005 0.082 1664 Dihedral : 22.089 179.779 2889 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.96 % Favored : 95.68 % Rotamer: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % 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: 0.43 (0.24), residues: 1111 helix: 1.54 (0.20), residues: 614 sheet: -0.58 (0.51), residues: 93 loop : -1.48 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 547 HIS 0.007 0.001 HIS A 868 PHE 0.032 0.003 PHE A1372 TYR 0.017 0.002 TYR A1593 ARG 0.012 0.001 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9675 (tp) cc_final: 0.9419 (mm) REVERT: A 474 LEU cc_start: 0.9369 (mm) cc_final: 0.9117 (pp) REVERT: A 684 PHE cc_start: 0.9589 (m-80) cc_final: 0.9287 (m-80) REVERT: A 799 GLU cc_start: 0.9305 (pt0) cc_final: 0.9079 (pt0) REVERT: A 865 MET cc_start: 0.7209 (pmm) cc_final: 0.6138 (tpp) REVERT: A 1026 MET cc_start: 0.8606 (mpp) cc_final: 0.8255 (mpp) REVERT: A 1408 MET cc_start: 0.9383 (mtm) cc_final: 0.9031 (mtp) REVERT: A 1416 MET cc_start: 0.9108 (mmt) cc_final: 0.8834 (mmm) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2433 time to fit residues: 28.7872 Evaluate side-chains 61 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 40.0000 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 GLN ** A1744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11701 Z= 0.235 Angle : 0.688 9.567 16300 Z= 0.357 Chirality : 0.040 0.239 1961 Planarity : 0.005 0.081 1664 Dihedral : 21.994 178.007 2889 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.59 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.24), residues: 1111 helix: 1.40 (0.20), residues: 612 sheet: -0.70 (0.53), residues: 93 loop : -1.61 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1528 HIS 0.011 0.002 HIS A 287 PHE 0.016 0.002 PHE A 785 TYR 0.012 0.002 TYR A1514 ARG 0.007 0.001 ARG A1788 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9678 (tp) cc_final: 0.9433 (mm) REVERT: A 548 CYS cc_start: 0.9347 (t) cc_final: 0.8624 (p) REVERT: A 1026 MET cc_start: 0.8630 (mpp) cc_final: 0.8299 (mpp) REVERT: A 1408 MET cc_start: 0.9358 (mtm) cc_final: 0.9119 (mtp) REVERT: A 1412 MET cc_start: 0.8809 (mtm) cc_final: 0.8508 (mtp) REVERT: A 1416 MET cc_start: 0.9081 (mmt) cc_final: 0.8810 (mmm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2129 time to fit residues: 23.3149 Evaluate side-chains 57 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 101 optimal weight: 40.0000 chunk 82 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 60 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1328 GLN A1744 GLN ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11701 Z= 0.202 Angle : 0.650 9.033 16300 Z= 0.337 Chirality : 0.039 0.246 1961 Planarity : 0.005 0.072 1664 Dihedral : 21.792 177.281 2889 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 29.16 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.50 % Favored : 95.14 % Rotamer: Outliers : 0.20 % Allowed : 3.66 % Favored : 96.13 % 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: 0.24 (0.25), residues: 1111 helix: 1.42 (0.21), residues: 613 sheet: -0.68 (0.53), residues: 93 loop : -1.64 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1528 HIS 0.011 0.001 HIS A 287 PHE 0.039 0.002 PHE A1372 TYR 0.013 0.001 TYR A1593 ARG 0.007 0.001 ARG A1788 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.8122 (mmm) cc_final: 0.7794 (mpp) REVERT: A 297 MET cc_start: 0.6874 (ptp) cc_final: 0.6490 (ptp) REVERT: A 434 LEU cc_start: 0.9669 (tp) cc_final: 0.9424 (mm) REVERT: A 548 CYS cc_start: 0.9367 (t) cc_final: 0.8804 (p) REVERT: A 1026 MET cc_start: 0.8668 (mpp) cc_final: 0.8264 (mpp) REVERT: A 1200 MET cc_start: 0.7718 (ptp) cc_final: 0.7067 (ppp) REVERT: A 1408 MET cc_start: 0.9305 (mtm) cc_final: 0.9056 (mtp) REVERT: A 1412 MET cc_start: 0.8582 (mtm) cc_final: 0.8241 (mtp) REVERT: A 1416 MET cc_start: 0.9097 (mmt) cc_final: 0.8821 (mmm) outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.2218 time to fit residues: 25.4584 Evaluate side-chains 60 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 98 optimal weight: 0.5980 chunk 55 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 433 ASN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5346 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11701 Z= 0.178 Angle : 0.621 9.606 16300 Z= 0.323 Chirality : 0.038 0.202 1961 Planarity : 0.004 0.064 1664 Dihedral : 21.507 176.186 2889 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.41 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 0.33 (0.25), residues: 1111 helix: 1.52 (0.21), residues: 613 sheet: -0.76 (0.54), residues: 98 loop : -1.61 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 547 HIS 0.007 0.001 HIS A 287 PHE 0.020 0.002 PHE A1372 TYR 0.016 0.001 TYR A 847 ARG 0.004 0.000 ARG A1741 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9649 (tp) cc_final: 0.9400 (mm) REVERT: A 548 CYS cc_start: 0.9395 (t) cc_final: 0.8877 (p) REVERT: A 1026 MET cc_start: 0.8667 (mpp) cc_final: 0.8282 (mpp) REVERT: A 1200 MET cc_start: 0.7732 (ptp) cc_final: 0.6979 (ppp) REVERT: A 1408 MET cc_start: 0.9330 (mtm) cc_final: 0.9094 (mtp) REVERT: A 1412 MET cc_start: 0.8662 (mtm) cc_final: 0.8333 (mtp) REVERT: A 1416 MET cc_start: 0.9104 (mmt) cc_final: 0.8831 (mmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2169 time to fit residues: 25.7214 Evaluate side-chains 57 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 40.0000 chunk 86 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 74 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 50.0000 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 333 GLN A 398 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 GLN ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5502 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11701 Z= 0.271 Angle : 0.724 9.216 16300 Z= 0.378 Chirality : 0.041 0.232 1961 Planarity : 0.005 0.082 1664 Dihedral : 21.941 176.120 2889 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 37.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.03 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -0.17 (0.25), residues: 1111 helix: 1.07 (0.21), residues: 614 sheet: -0.83 (0.56), residues: 93 loop : -1.80 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1528 HIS 0.009 0.002 HIS A1611 PHE 0.029 0.003 PHE A 785 TYR 0.018 0.002 TYR A 327 ARG 0.014 0.001 ARG A1788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.7957 (mmm) cc_final: 0.7264 (mpp) REVERT: A 297 MET cc_start: 0.6968 (ptp) cc_final: 0.6261 (ptp) REVERT: A 411 MET cc_start: 0.8555 (mpp) cc_final: 0.8321 (mpp) REVERT: A 434 LEU cc_start: 0.9720 (tp) cc_final: 0.9483 (mm) REVERT: A 1026 MET cc_start: 0.8668 (mpp) cc_final: 0.8358 (mpp) REVERT: A 1200 MET cc_start: 0.7879 (ptp) cc_final: 0.7246 (ppp) REVERT: A 1408 MET cc_start: 0.9342 (mtm) cc_final: 0.9071 (mtp) REVERT: A 1412 MET cc_start: 0.8721 (mtm) cc_final: 0.8395 (mtp) REVERT: A 1416 MET cc_start: 0.9113 (mmt) cc_final: 0.8871 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2298 time to fit residues: 26.3434 Evaluate side-chains 54 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.0870 chunk 35 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1776 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11701 Z= 0.164 Angle : 0.622 8.937 16300 Z= 0.319 Chirality : 0.038 0.195 1961 Planarity : 0.004 0.055 1664 Dihedral : 21.415 173.961 2889 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.68 % Favored : 94.87 % Rotamer: Outliers : 0.10 % Allowed : 1.32 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.25), residues: 1111 helix: 1.39 (0.21), residues: 619 sheet: -0.57 (0.63), residues: 75 loop : -1.73 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 341 HIS 0.008 0.001 HIS A 287 PHE 0.021 0.002 PHE A 846 TYR 0.010 0.001 TYR A 550 ARG 0.009 0.000 ARG A1788 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9691 (tp) cc_final: 0.9460 (mm) REVERT: A 548 CYS cc_start: 0.9310 (t) cc_final: 0.8797 (p) REVERT: A 794 GLU cc_start: 0.9600 (mm-30) cc_final: 0.9383 (pt0) REVERT: A 865 MET cc_start: 0.7194 (pmm) cc_final: 0.6123 (tpt) REVERT: A 1026 MET cc_start: 0.8721 (mpp) cc_final: 0.8386 (mpp) REVERT: A 1200 MET cc_start: 0.7809 (ptp) cc_final: 0.7041 (ppp) REVERT: A 1408 MET cc_start: 0.9315 (mtm) cc_final: 0.9061 (mtp) REVERT: A 1412 MET cc_start: 0.8604 (mtm) cc_final: 0.8338 (mtp) REVERT: A 1416 MET cc_start: 0.9017 (mmt) cc_final: 0.8750 (mmm) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.2310 time to fit residues: 27.7056 Evaluate side-chains 59 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 40.0000 chunk 72 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5441 moved from start: 0.7497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11701 Z= 0.225 Angle : 0.669 8.594 16300 Z= 0.350 Chirality : 0.040 0.245 1961 Planarity : 0.005 0.056 1664 Dihedral : 21.522 174.678 2889 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.49 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -0.01 (0.25), residues: 1111 helix: 1.31 (0.21), residues: 613 sheet: -1.11 (0.53), residues: 98 loop : -1.83 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1528 HIS 0.007 0.001 HIS A 398 PHE 0.045 0.002 PHE A1372 TYR 0.012 0.001 TYR A1252 ARG 0.015 0.001 ARG A1788 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9717 (tp) cc_final: 0.9498 (mm) REVERT: A 774 MET cc_start: 0.8703 (pmm) cc_final: 0.8467 (mpp) REVERT: A 794 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9436 (pt0) REVERT: A 1026 MET cc_start: 0.8681 (mpp) cc_final: 0.8357 (mpp) REVERT: A 1200 MET cc_start: 0.7776 (ptp) cc_final: 0.6973 (ppp) REVERT: A 1412 MET cc_start: 0.8608 (mtm) cc_final: 0.8317 (mtp) REVERT: A 1416 MET cc_start: 0.9120 (mmt) cc_final: 0.8852 (mmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2196 time to fit residues: 24.2114 Evaluate side-chains 55 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 50.0000 chunk 55 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 112 optimal weight: 40.0000 chunk 97 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 103 optimal weight: 0.0470 overall best weight: 6.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.7938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11701 Z= 0.228 Angle : 0.688 9.042 16300 Z= 0.356 Chirality : 0.040 0.227 1961 Planarity : 0.005 0.057 1664 Dihedral : 21.664 173.161 2889 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 31.33 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.94 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.26 (0.25), residues: 1111 helix: 1.11 (0.21), residues: 625 sheet: -1.26 (0.54), residues: 93 loop : -2.03 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A1528 HIS 0.008 0.001 HIS A 398 PHE 0.034 0.002 PHE A1372 TYR 0.012 0.002 TYR A1514 ARG 0.010 0.001 ARG A1788 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1026 MET cc_start: 0.8738 (mpp) cc_final: 0.8423 (mpp) REVERT: A 1200 MET cc_start: 0.7931 (ptp) cc_final: 0.6780 (ppp) REVERT: A 1408 MET cc_start: 0.9444 (mpp) cc_final: 0.9244 (mpp) REVERT: A 1412 MET cc_start: 0.8615 (mtm) cc_final: 0.8306 (mtp) REVERT: A 1416 MET cc_start: 0.9045 (mmt) cc_final: 0.8777 (mmm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2220 time to fit residues: 25.0608 Evaluate side-chains 55 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 100 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.040289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.030505 restraints weight = 185261.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.030985 restraints weight = 148397.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.031358 restraints weight = 126334.879| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11701 Z= 0.190 Angle : 0.650 9.077 16300 Z= 0.335 Chirality : 0.039 0.204 1961 Planarity : 0.004 0.047 1664 Dihedral : 21.463 172.479 2889 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 26.98 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.31 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.25), residues: 1111 helix: 1.21 (0.21), residues: 627 sheet: -1.21 (0.56), residues: 84 loop : -1.85 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1528 HIS 0.006 0.001 HIS A 398 PHE 0.026 0.002 PHE A1372 TYR 0.017 0.001 TYR A1352 ARG 0.003 0.000 ARG A1628 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.72 seconds wall clock time: 35 minutes 17.56 seconds (2117.56 seconds total)