Starting phenix.real_space_refine on Sun Apr 27 11:11:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw7_48691/04_2025/9mw7_48691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw7_48691/04_2025/9mw7_48691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mw7_48691/04_2025/9mw7_48691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw7_48691/04_2025/9mw7_48691.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw7_48691/04_2025/9mw7_48691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw7_48691/04_2025/9mw7_48691.cif" } resolution = 3.4 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= 0.010 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 Al 1 5.89 5 P 54 5.49 5 S 23 5.16 5 C 3269 2.51 5 N 963 2.21 5 O 1191 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5504 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 566 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 14} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "C" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 573 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4334 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 25, 'TRANS': 509} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.82 Number of scatterers: 5504 At special positions: 0 Unit cell: (74.12, 88.944, 106.384, 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) S 23 16.00 P 54 15.00 Al 1 13.00 F 3 9.00 O 1191 8.00 N 963 7.00 C 3269 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 757.0 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 44.9% alpha, 9.5% beta 23 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.694A pdb=" N VAL A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 17 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 removed outlier: 4.318A pdb=" N VAL A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.660A pdb=" N ILE A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 removed outlier: 3.960A pdb=" N VAL A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.517A pdb=" N MET A 95 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP A 100 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.725A pdb=" N PHE A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.746A pdb=" N HIS A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 376 through 393 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.529A pdb=" N TYR A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.687A pdb=" N ASP A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.916A pdb=" N ASP A 544 " --> pdb=" O TYR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 613 through 632 removed outlier: 4.562A pdb=" N GLU A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ALA A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 644 removed outlier: 3.742A pdb=" N LYS A 643 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 644 " --> pdb=" O PRO A 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 644' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 5.880A pdb=" N ILE A 28 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.869A pdb=" N VAL A 116 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 63 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET A 117 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N PHE A 65 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ARG A 62 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 138 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 140 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG A 170 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 228 removed outlier: 4.083A pdb=" N ILE A 488 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 226 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 490 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 371 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP A 404 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 581 removed outlier: 3.645A pdb=" N THR A 577 " --> pdb=" O THR A 593 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1536 1.34 - 1.46: 1174 1.46 - 1.57: 2864 1.57 - 1.69: 110 1.69 - 1.81: 35 Bond restraints: 5719 Sorted by residual: bond pdb=" N LYS A 149 " pdb=" CA LYS A 149 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" C4 ADP A 702 " pdb=" C5 ADP A 702 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" CB LYS A 628 " pdb=" CG LYS A 628 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" C VAL A 406 " pdb=" O VAL A 406 " ideal model delta sigma weight residual 1.245 1.231 0.014 1.41e-02 5.03e+03 9.95e-01 bond pdb=" C VAL A 448 " pdb=" O VAL A 448 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 8.05e-01 ... (remaining 5714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 7826 1.97 - 3.95: 113 3.95 - 5.92: 21 5.92 - 7.90: 5 7.90 - 9.87: 1 Bond angle restraints: 7966 Sorted by residual: angle pdb=" C PRO A 641 " pdb=" N VAL A 642 " pdb=" CA VAL A 642 " ideal model delta sigma weight residual 121.97 127.06 -5.09 1.80e+00 3.09e-01 8.00e+00 angle pdb=" CA LEU A 44 " pdb=" CB LEU A 44 " pdb=" CG LEU A 44 " ideal model delta sigma weight residual 116.30 126.17 -9.87 3.50e+00 8.16e-02 7.96e+00 angle pdb=" CA LYS A 628 " pdb=" CB LYS A 628 " pdb=" CG LYS A 628 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.52e+00 angle pdb=" C LYS A 482 " pdb=" N ASN A 483 " pdb=" CA ASN A 483 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.15e+00 angle pdb=" C LYS A 149 " pdb=" CA LYS A 149 " pdb=" CB LYS A 149 " ideal model delta sigma weight residual 110.42 115.46 -5.04 1.99e+00 2.53e-01 6.40e+00 ... (remaining 7961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 3035 17.29 - 34.58: 331 34.58 - 51.87: 126 51.87 - 69.16: 69 69.16 - 86.45: 17 Dihedral angle restraints: 3578 sinusoidal: 1998 harmonic: 1580 Sorted by residual: dihedral pdb=" CA ASP A 395 " pdb=" CB ASP A 395 " pdb=" CG ASP A 395 " pdb=" OD1 ASP A 395 " ideal model delta sinusoidal sigma weight residual -30.00 -89.25 59.25 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CG ARG A 547 " pdb=" CD ARG A 547 " pdb=" NE ARG A 547 " pdb=" CZ ARG A 547 " ideal model delta sinusoidal sigma weight residual 180.00 135.76 44.24 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CB GLU A 533 " pdb=" CG GLU A 533 " pdb=" CD GLU A 533 " pdb=" OE1 GLU A 533 " ideal model delta sinusoidal sigma weight residual 0.00 86.45 -86.45 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 3575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 654 0.030 - 0.060: 184 0.060 - 0.091: 48 0.091 - 0.121: 38 0.121 - 0.151: 6 Chirality restraints: 930 Sorted by residual: chirality pdb=" CG LEU A 387 " pdb=" CB LEU A 387 " pdb=" CD1 LEU A 387 " pdb=" CD2 LEU A 387 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" C1' ADP A 702 " pdb=" C2' ADP A 702 " pdb=" N9 ADP A 702 " pdb=" O4' ADP A 702 " both_signs ideal model delta sigma weight residual False 2.48 2.63 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA ASN A 483 " pdb=" N ASN A 483 " pdb=" C ASN A 483 " pdb=" CB ASN A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 927 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 220 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 221 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B 26 " 0.020 2.00e-02 2.50e+03 1.11e-02 2.76e+00 pdb=" N1 C B 26 " -0.026 2.00e-02 2.50e+03 pdb=" C2 C B 26 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C B 26 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C B 26 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C B 26 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B 26 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C B 26 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C B 26 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 10 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 11 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " -0.022 5.00e-02 4.00e+02 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 217 2.69 - 3.24: 5539 3.24 - 3.80: 9303 3.80 - 4.35: 11697 4.35 - 4.90: 17246 Nonbonded interactions: 44002 Sorted by model distance: nonbonded pdb=" F1 AF3 A 701 " pdb=" O1B ADP A 702 " model vdw 2.138 2.990 nonbonded pdb=" O ILE A 80 " pdb=" OG1 THR A 84 " model vdw 2.179 3.040 nonbonded pdb=" O ILE A 554 " pdb=" ND1 HIS A 558 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 108 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR A 14 " pdb=" O SER A 35 " model vdw 2.257 3.040 ... (remaining 43997 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: 2.590 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: 19.670 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 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 : 0.008 0.608 5721 Z= 0.812 Angle : 0.619 9.873 7966 Z= 0.307 Chirality : 0.037 0.151 930 Planarity : 0.004 0.043 821 Dihedral : 18.410 86.451 2548 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.23 % Favored : 90.58 % Rotamer: Outliers : 1.01 % Allowed : 21.50 % Favored : 77.48 % 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: -1.07 (0.37), residues: 531 helix: 0.58 (0.38), residues: 198 sheet: -0.20 (0.61), residues: 80 loop : -1.99 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 105 HIS 0.003 0.001 HIS A 145 PHE 0.016 0.001 PHE A 39 TYR 0.012 0.001 TYR A 560 ARG 0.001 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.14973 ( 203) hydrogen bonds : angle 5.37551 ( 534) covalent geometry : bond 0.00237 ( 5719) covalent geometry : angle 0.61946 ( 7966) Misc. bond : bond 0.42960 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8648 (mm) cc_final: 0.8211 (pp) REVERT: A 422 MET cc_start: 0.7759 (ppp) cc_final: 0.7218 (ppp) REVERT: A 468 ASN cc_start: 0.7961 (p0) cc_final: 0.7633 (m-40) REVERT: A 489 MET cc_start: 0.5951 (mmp) cc_final: 0.5567 (mmm) REVERT: A 550 MET cc_start: 0.7098 (ppp) cc_final: 0.6494 (ppp) REVERT: A 558 HIS cc_start: 0.8063 (m90) cc_final: 0.7603 (m90) REVERT: A 615 LYS cc_start: 0.8138 (tptt) cc_final: 0.7129 (tptp) REVERT: A 632 MET cc_start: 0.2449 (ptm) cc_final: 0.1933 (ptm) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.2270 time to fit residues: 11.1389 Evaluate side-chains 38 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 554 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 127 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.108542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.085446 restraints weight = 27318.825| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 5.84 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5721 Z= 0.169 Angle : 0.665 9.342 7966 Z= 0.328 Chirality : 0.040 0.181 930 Planarity : 0.005 0.044 821 Dihedral : 16.870 75.918 1409 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.26 % Allowed : 19.27 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.37), residues: 531 helix: 0.22 (0.36), residues: 207 sheet: -1.05 (0.56), residues: 85 loop : -2.10 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.005 0.002 HIS A 128 PHE 0.013 0.002 PHE A 65 TYR 0.013 0.002 TYR A 560 ARG 0.008 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 203) hydrogen bonds : angle 4.78755 ( 534) covalent geometry : bond 0.00368 ( 5719) covalent geometry : angle 0.66519 ( 7966) Misc. bond : bond 0.00363 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.6566 (ttt180) cc_final: 0.6137 (ttt180) REVERT: A 362 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6530 (p0) REVERT: A 422 MET cc_start: 0.7395 (ppp) cc_final: 0.7007 (ppp) REVERT: A 468 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7609 (m-40) REVERT: A 550 MET cc_start: 0.7179 (ppp) cc_final: 0.6481 (ppp) REVERT: A 558 HIS cc_start: 0.8502 (m90) cc_final: 0.8101 (m90) REVERT: A 615 LYS cc_start: 0.8026 (tptt) cc_final: 0.7042 (tptp) REVERT: A 632 MET cc_start: 0.2966 (ptm) cc_final: 0.1784 (ptm) outliers start: 21 outliers final: 9 residues processed: 48 average time/residue: 0.2119 time to fit residues: 13.2905 Evaluate side-chains 41 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 582 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.110019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.087631 restraints weight = 27928.667| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 5.19 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5721 Z= 0.117 Angle : 0.612 10.248 7966 Z= 0.296 Chirality : 0.038 0.144 930 Planarity : 0.004 0.038 821 Dihedral : 16.758 75.409 1402 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.84 % Allowed : 19.68 % Favored : 77.48 % 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: -1.40 (0.37), residues: 531 helix: 0.25 (0.36), residues: 208 sheet: -1.11 (0.58), residues: 79 loop : -1.92 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.005 0.001 HIS A 409 PHE 0.009 0.001 PHE A 463 TYR 0.015 0.001 TYR A 560 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 203) hydrogen bonds : angle 4.48183 ( 534) covalent geometry : bond 0.00245 ( 5719) covalent geometry : angle 0.61237 ( 7966) Misc. bond : bond 0.00322 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8646 (mm) cc_final: 0.8028 (pp) REVERT: A 422 MET cc_start: 0.7356 (ppp) cc_final: 0.7148 (ppp) REVERT: A 468 ASN cc_start: 0.7969 (p0) cc_final: 0.7600 (m-40) REVERT: A 550 MET cc_start: 0.7214 (ppp) cc_final: 0.6527 (ppp) REVERT: A 558 HIS cc_start: 0.7989 (m90) cc_final: 0.7554 (m90) REVERT: A 632 MET cc_start: 0.2741 (ptm) cc_final: 0.1446 (ptm) outliers start: 14 outliers final: 7 residues processed: 44 average time/residue: 0.2311 time to fit residues: 13.6909 Evaluate side-chains 39 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 458 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 40 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.106138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.083359 restraints weight = 28282.294| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 5.18 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5721 Z= 0.213 Angle : 0.743 11.134 7966 Z= 0.369 Chirality : 0.043 0.196 930 Planarity : 0.005 0.043 821 Dihedral : 17.258 76.435 1402 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.86 % Favored : 87.95 % Rotamer: Outliers : 3.85 % Allowed : 20.49 % Favored : 75.66 % 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: -1.98 (0.36), residues: 531 helix: -0.25 (0.34), residues: 206 sheet: -1.60 (0.52), residues: 84 loop : -2.14 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 105 HIS 0.005 0.002 HIS A 638 PHE 0.015 0.002 PHE A 405 TYR 0.013 0.002 TYR A 560 ARG 0.003 0.000 ARG A 595 Details of bonding type rmsd hydrogen bonds : bond 0.05336 ( 203) hydrogen bonds : angle 5.03661 ( 534) covalent geometry : bond 0.00465 ( 5719) covalent geometry : angle 0.74350 ( 7966) Misc. bond : bond 0.00339 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: A 362 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.6369 (p0) REVERT: A 422 MET cc_start: 0.7291 (ppp) cc_final: 0.6916 (ppp) REVERT: A 550 MET cc_start: 0.7193 (ppp) cc_final: 0.6609 (ppp) REVERT: A 558 HIS cc_start: 0.8295 (m90) cc_final: 0.7827 (m90) REVERT: A 615 LYS cc_start: 0.8032 (tptt) cc_final: 0.7745 (ptmt) REVERT: A 632 MET cc_start: 0.3008 (ptm) cc_final: 0.2359 (ptm) outliers start: 19 outliers final: 12 residues processed: 49 average time/residue: 0.2029 time to fit residues: 13.0110 Evaluate side-chains 45 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 582 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 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 = 0.4461 r_free = 0.4461 target = 0.108099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.085839 restraints weight = 27805.526| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 5.08 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5721 Z= 0.127 Angle : 0.651 11.092 7966 Z= 0.316 Chirality : 0.039 0.158 930 Planarity : 0.004 0.040 821 Dihedral : 17.153 75.408 1402 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.45 % Allowed : 21.30 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.76 (0.37), residues: 531 helix: 0.03 (0.36), residues: 206 sheet: -1.45 (0.55), residues: 84 loop : -2.12 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 PHE 0.010 0.001 PHE A 463 TYR 0.015 0.001 TYR A 560 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 203) hydrogen bonds : angle 4.51848 ( 534) covalent geometry : bond 0.00274 ( 5719) covalent geometry : angle 0.65113 ( 7966) Misc. bond : bond 0.00343 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.6298 (p0) REVERT: A 468 ASN cc_start: 0.8012 (p0) cc_final: 0.7688 (m-40) REVERT: A 550 MET cc_start: 0.7100 (ppp) cc_final: 0.6539 (ppp) REVERT: A 558 HIS cc_start: 0.8018 (m90) cc_final: 0.7544 (m90) REVERT: A 587 ASN cc_start: 0.8145 (m-40) cc_final: 0.7923 (p0) REVERT: A 615 LYS cc_start: 0.8038 (tptt) cc_final: 0.7125 (tptp) REVERT: A 632 MET cc_start: 0.2962 (ptm) cc_final: 0.2285 (ptm) outliers start: 17 outliers final: 10 residues processed: 46 average time/residue: 0.2089 time to fit residues: 12.5679 Evaluate side-chains 44 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 575 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.109304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.087713 restraints weight = 27657.739| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 5.03 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5721 Z= 0.116 Angle : 0.631 10.526 7966 Z= 0.303 Chirality : 0.038 0.162 930 Planarity : 0.004 0.036 821 Dihedral : 16.888 75.011 1402 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 2.84 % Allowed : 22.31 % Favored : 74.85 % 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: -1.51 (0.37), residues: 531 helix: 0.27 (0.37), residues: 207 sheet: -1.48 (0.58), residues: 79 loop : -1.96 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 PHE 0.008 0.001 PHE A 463 TYR 0.016 0.001 TYR A 560 ARG 0.002 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 203) hydrogen bonds : angle 4.19806 ( 534) covalent geometry : bond 0.00245 ( 5719) covalent geometry : angle 0.63090 ( 7966) Misc. bond : bond 0.00358 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ASN cc_start: 0.7972 (p0) cc_final: 0.7617 (m-40) REVERT: A 550 MET cc_start: 0.7078 (ppp) cc_final: 0.6507 (ppp) REVERT: A 558 HIS cc_start: 0.8026 (m90) cc_final: 0.7488 (m90) REVERT: A 632 MET cc_start: 0.2812 (OUTLIER) cc_final: 0.1753 (tmm) outliers start: 14 outliers final: 5 residues processed: 42 average time/residue: 0.2067 time to fit residues: 11.4451 Evaluate side-chains 37 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 632 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 3 optimal weight: 8.9990 chunk 18 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 458 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.109879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.088358 restraints weight = 27668.824| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 5.08 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5721 Z= 0.111 Angle : 0.627 10.704 7966 Z= 0.299 Chirality : 0.038 0.154 930 Planarity : 0.004 0.035 821 Dihedral : 16.762 74.920 1402 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.85 % Favored : 90.77 % Rotamer: Outliers : 1.83 % Allowed : 22.92 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.38 (0.37), residues: 531 helix: 0.41 (0.37), residues: 207 sheet: -1.40 (0.59), residues: 78 loop : -1.93 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 PHE 0.008 0.001 PHE A 141 TYR 0.016 0.001 TYR A 560 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 203) hydrogen bonds : angle 4.08790 ( 534) covalent geometry : bond 0.00236 ( 5719) covalent geometry : angle 0.62710 ( 7966) Misc. bond : bond 0.00333 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 468 ASN cc_start: 0.7549 (p0) cc_final: 0.7230 (m-40) REVERT: A 550 MET cc_start: 0.7097 (ppp) cc_final: 0.6436 (ppp) REVERT: A 558 HIS cc_start: 0.8367 (m90) cc_final: 0.7794 (m90) REVERT: A 632 MET cc_start: 0.2894 (OUTLIER) cc_final: 0.1923 (tmm) outliers start: 9 outliers final: 6 residues processed: 38 average time/residue: 0.2160 time to fit residues: 11.0229 Evaluate side-chains 37 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 632 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 38 optimal weight: 0.0070 chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.107568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.085450 restraints weight = 27675.623| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 5.05 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5721 Z= 0.166 Angle : 0.696 10.237 7966 Z= 0.338 Chirality : 0.041 0.177 930 Planarity : 0.005 0.047 821 Dihedral : 16.947 75.696 1402 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.11 % Favored : 88.51 % Rotamer: Outliers : 2.23 % Allowed : 22.92 % Favored : 74.85 % 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: -1.58 (0.37), residues: 531 helix: 0.22 (0.36), residues: 207 sheet: -1.60 (0.58), residues: 78 loop : -1.97 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 105 HIS 0.006 0.002 HIS A 128 PHE 0.013 0.002 PHE A 405 TYR 0.017 0.002 TYR A 91 ARG 0.007 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 203) hydrogen bonds : angle 4.53202 ( 534) covalent geometry : bond 0.00363 ( 5719) covalent geometry : angle 0.69594 ( 7966) Misc. bond : bond 0.00321 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 422 MET cc_start: 0.8599 (pmm) cc_final: 0.8357 (pmm) REVERT: A 550 MET cc_start: 0.7107 (ppp) cc_final: 0.6656 (ppp) REVERT: A 558 HIS cc_start: 0.8114 (m90) cc_final: 0.7585 (m90) REVERT: A 632 MET cc_start: 0.3207 (OUTLIER) cc_final: 0.2203 (tmm) outliers start: 11 outliers final: 8 residues processed: 37 average time/residue: 0.2619 time to fit residues: 12.9749 Evaluate side-chains 37 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 632 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 0.0020 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.108412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.086091 restraints weight = 27848.648| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 5.16 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5721 Z= 0.138 Angle : 0.676 10.523 7966 Z= 0.325 Chirality : 0.039 0.148 930 Planarity : 0.004 0.037 821 Dihedral : 17.007 75.406 1402 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.36 % Favored : 89.27 % Rotamer: Outliers : 2.23 % Allowed : 23.12 % Favored : 74.65 % 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: -1.59 (0.37), residues: 531 helix: 0.22 (0.36), residues: 206 sheet: -1.66 (0.58), residues: 78 loop : -1.95 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 PHE 0.011 0.002 PHE A 463 TYR 0.014 0.001 TYR A 560 ARG 0.007 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 203) hydrogen bonds : angle 4.43667 ( 534) covalent geometry : bond 0.00301 ( 5719) covalent geometry : angle 0.67572 ( 7966) Misc. bond : bond 0.00322 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ASN cc_start: 0.7950 (p0) cc_final: 0.7593 (m-40) REVERT: A 550 MET cc_start: 0.7106 (ppp) cc_final: 0.6748 (ppp) REVERT: A 558 HIS cc_start: 0.8075 (m90) cc_final: 0.7506 (m90) REVERT: A 632 MET cc_start: 0.3410 (OUTLIER) cc_final: 0.2328 (tmm) outliers start: 11 outliers final: 8 residues processed: 36 average time/residue: 0.2373 time to fit residues: 11.5510 Evaluate side-chains 41 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 632 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.109381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.087149 restraints weight = 27501.059| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 5.03 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5721 Z= 0.117 Angle : 0.662 11.533 7966 Z= 0.315 Chirality : 0.039 0.191 930 Planarity : 0.004 0.036 821 Dihedral : 16.898 75.034 1402 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.23 % Favored : 90.40 % Rotamer: Outliers : 1.62 % Allowed : 23.73 % Favored : 74.65 % 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: -1.46 (0.37), residues: 531 helix: 0.36 (0.37), residues: 206 sheet: -1.44 (0.61), residues: 78 loop : -1.97 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 PHE 0.008 0.001 PHE A 141 TYR 0.014 0.001 TYR A 560 ARG 0.007 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 203) hydrogen bonds : angle 4.26727 ( 534) covalent geometry : bond 0.00251 ( 5719) covalent geometry : angle 0.66155 ( 7966) Misc. bond : bond 0.00321 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 468 ASN cc_start: 0.7948 (p0) cc_final: 0.7575 (m-40) REVERT: A 550 MET cc_start: 0.7232 (ppp) cc_final: 0.6717 (ppp) REVERT: A 632 MET cc_start: 0.3243 (OUTLIER) cc_final: 0.1999 (ptt) outliers start: 8 outliers final: 5 residues processed: 35 average time/residue: 0.2795 time to fit residues: 13.4335 Evaluate side-chains 36 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 632 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.0270 chunk 39 optimal weight: 0.0030 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.109890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.087495 restraints weight = 27715.956| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 5.46 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5721 Z= 0.112 Angle : 0.638 10.794 7966 Z= 0.305 Chirality : 0.038 0.177 930 Planarity : 0.004 0.036 821 Dihedral : 16.785 74.946 1402 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.04 % Favored : 90.58 % Rotamer: Outliers : 1.22 % Allowed : 23.73 % Favored : 75.05 % 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: -1.40 (0.37), residues: 531 helix: 0.44 (0.37), residues: 208 sheet: -1.50 (0.60), residues: 79 loop : -1.94 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 PHE 0.009 0.001 PHE A 469 TYR 0.015 0.001 TYR A 560 ARG 0.007 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 203) hydrogen bonds : angle 4.14679 ( 534) covalent geometry : bond 0.00240 ( 5719) covalent geometry : angle 0.63816 ( 7966) Misc. bond : bond 0.00309 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.49 seconds wall clock time: 60 minutes 42.03 seconds (3642.03 seconds total)