Starting phenix.real_space_refine on Fri Dec 27 16:52:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1j_34428/12_2024/8h1j_34428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1j_34428/12_2024/8h1j_34428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h1j_34428/12_2024/8h1j_34428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1j_34428/12_2024/8h1j_34428.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1j_34428/12_2024/8h1j_34428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1j_34428/12_2024/8h1j_34428.cif" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.134 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 134 5.49 5 S 6 5.16 5 C 3147 2.51 5 N 1063 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5773 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2930 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "B" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2185 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 52, 'rna3p_pyr': 43} Link IDs: {'rna2p': 7, 'rna3p': 94} Chain breaks: 2 Chain: "D" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2567 SG CYS A 331 56.562 13.710 50.711 1.00192.35 S ATOM 2591 SG CYS A 334 56.015 10.341 49.439 1.00215.36 S ATOM 2728 SG CYS A 351 54.453 10.050 52.311 1.00222.37 S ATOM 2749 SG CYS A 354 57.190 11.215 52.766 1.00225.00 S Time building chain proxies: 4.24, per 1000 atoms: 0.73 Number of scatterers: 5773 At special positions: 0 Unit cell: (77.024, 102.256, 104.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 6 16.00 P 134 15.00 O 1422 8.00 N 1063 7.00 C 3147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 578.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 351 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 354 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 334 " Number of angles added : 6 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 674 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 4 sheets defined 48.6% alpha, 20.4% beta 57 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 14 through 47 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.857A pdb=" N LEU A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.711A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.935A pdb=" N GLU A 116 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LYS A 153 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU A 176 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 155 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLU A 174 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A 157 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 172 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 159 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 170 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ARG A 161 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU A 168 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 163 " --> pdb=" O HIS A 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 10 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 128 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.761A pdb=" N PHE A 186 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU A 278 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU A 273 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER A 319 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 275 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 321 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 277 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 351 removed outlier: 3.918A pdb=" N TRP A 349 " --> pdb=" O HIS A 358 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1031 1.33 - 1.45: 2200 1.45 - 1.57: 2666 1.57 - 1.69: 263 1.69 - 1.81: 7 Bond restraints: 6167 Sorted by residual: bond pdb=" C1' G B -45 " pdb=" N9 G B -45 " ideal model delta sigma weight residual 1.475 1.455 0.020 1.50e-02 4.44e+03 1.78e+00 bond pdb=" O5' C B-107 " pdb=" C5' C B-107 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.64e+00 bond pdb=" N9 G B -45 " pdb=" C4 G B -45 " ideal model delta sigma weight residual 1.375 1.400 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.41e+00 bond pdb=" C5 DC D -8 " pdb=" C6 DC D -8 " ideal model delta sigma weight residual 1.337 1.360 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 6162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 8152 0.85 - 1.71: 663 1.71 - 2.56: 102 2.56 - 3.41: 26 3.41 - 4.27: 9 Bond angle restraints: 8952 Sorted by residual: angle pdb=" N VAL A 346 " pdb=" CA VAL A 346 " pdb=" C VAL A 346 " ideal model delta sigma weight residual 106.21 109.76 -3.55 1.07e+00 8.73e-01 1.10e+01 angle pdb=" O3' C B-107 " pdb=" C3' C B-107 " pdb=" C2' C B-107 " ideal model delta sigma weight residual 113.70 109.43 4.27 1.50e+00 4.44e-01 8.09e+00 angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 118.12 -4.22 1.80e+00 3.09e-01 5.49e+00 angle pdb=" C HIS A 34 " pdb=" N PHE A 35 " pdb=" CA PHE A 35 " ideal model delta sigma weight residual 121.14 117.32 3.82 1.75e+00 3.27e-01 4.76e+00 angle pdb=" CA VAL A 346 " pdb=" C VAL A 346 " pdb=" O VAL A 346 " ideal model delta sigma weight residual 122.63 120.76 1.87 8.70e-01 1.32e+00 4.64e+00 ... (remaining 8947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 3010 18.12 - 36.25: 360 36.25 - 54.37: 229 54.37 - 72.49: 140 72.49 - 90.62: 27 Dihedral angle restraints: 3766 sinusoidal: 2717 harmonic: 1049 Sorted by residual: dihedral pdb=" CA PHE A 35 " pdb=" C PHE A 35 " pdb=" N LEU A 36 " pdb=" CA LEU A 36 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " ideal model delta sinusoidal sigma weight residual -180.00 -120.80 -59.20 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 143 " pdb=" CB LYS A 143 " pdb=" CG LYS A 143 " pdb=" CD LYS A 143 " ideal model delta sinusoidal sigma weight residual -60.00 -118.40 58.40 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 3763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 805 0.033 - 0.067: 201 0.067 - 0.100: 47 0.100 - 0.134: 13 0.134 - 0.167: 4 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C1' A B -88 " pdb=" O4' A B -88 " pdb=" C2' A B -88 " pdb=" N9 A B -88 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C3' C B-107 " pdb=" C4' C B-107 " pdb=" O3' C B-107 " pdb=" C2' C B-107 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1067 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 21 " -0.029 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 DA C 21 " 0.005 2.00e-02 2.50e+03 pdb=" C8 DA C 21 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DA C 21 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA C 21 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DA C 21 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA C 21 " -0.022 2.00e-02 2.50e+03 pdb=" N1 DA C 21 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA C 21 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA C 21 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA C 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -96 " -0.026 2.00e-02 2.50e+03 1.09e-02 3.58e+00 pdb=" N9 G B -96 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G B -96 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B -96 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B -96 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B -96 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B -96 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B -96 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B -96 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B -96 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B -96 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G B -96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 106 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 107 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.025 5.00e-02 4.00e+02 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1045 2.77 - 3.30: 5147 3.30 - 3.83: 11172 3.83 - 4.37: 13054 4.37 - 4.90: 18820 Nonbonded interactions: 49238 Sorted by model distance: nonbonded pdb=" N2 G B-112 " pdb=" N6 A B -86 " model vdw 2.232 2.560 nonbonded pdb=" O2' G B-111 " pdb=" N4 C B -85 " model vdw 2.293 3.120 nonbonded pdb=" NH1 ARG A 270 " pdb=" OP1 A B -1 " model vdw 2.303 3.120 nonbonded pdb=" NH1 ARG A 110 " pdb=" OP1 C B 5 " model vdw 2.347 3.120 nonbonded pdb=" OG1 THR A 114 " pdb=" OP1 DA C 8 " model vdw 2.356 3.040 ... (remaining 49233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 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 : 0.005 0.044 6167 Z= 0.287 Angle : 0.533 4.266 8952 Z= 0.306 Chirality : 0.034 0.167 1070 Planarity : 0.004 0.044 648 Dihedral : 22.060 90.616 3092 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.19 % Allowed : 9.74 % Favored : 85.06 % 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: 2.19 (0.45), residues: 358 helix: 2.39 (0.37), residues: 173 sheet: 0.49 (0.60), residues: 81 loop : 0.79 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 349 HIS 0.005 0.001 HIS A 163 PHE 0.026 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.6814 (tp) cc_final: 0.6588 (tt) REVERT: A 48 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6282 (pttt) REVERT: A 58 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7176 (tt0) REVERT: A 95 ARG cc_start: 0.5955 (ttt90) cc_final: 0.5608 (ttp-110) REVERT: A 121 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: A 149 ASP cc_start: 0.7883 (m-30) cc_final: 0.7430 (t70) REVERT: A 175 VAL cc_start: 0.7996 (t) cc_final: 0.7731 (m) REVERT: A 205 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6226 (mtm110) REVERT: A 207 LYS cc_start: 0.7279 (tptm) cc_final: 0.6720 (ttmt) REVERT: A 210 GLN cc_start: 0.8743 (pt0) cc_final: 0.8465 (pt0) REVERT: A 233 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5044 (mmtt) REVERT: A 245 LYS cc_start: 0.7923 (tttt) cc_final: 0.7696 (mttm) REVERT: A 248 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7114 (tpt-90) REVERT: A 252 ARG cc_start: 0.6381 (mtt180) cc_final: 0.5898 (mtp-110) REVERT: A 349 TRP cc_start: 0.7735 (p-90) cc_final: 0.5851 (p-90) REVERT: A 367 ASN cc_start: 0.6759 (m-40) cc_final: 0.6497 (m-40) REVERT: A 371 GLU cc_start: 0.7470 (tp30) cc_final: 0.7177 (tp30) outliers start: 16 outliers final: 7 residues processed: 69 average time/residue: 0.2880 time to fit residues: 23.6629 Evaluate side-chains 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6167 Z= 0.157 Angle : 0.462 4.480 8952 Z= 0.257 Chirality : 0.032 0.150 1070 Planarity : 0.004 0.042 648 Dihedral : 22.871 93.936 2380 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.22 % Allowed : 11.69 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.51 (0.46), residues: 358 helix: 2.68 (0.37), residues: 175 sheet: 0.68 (0.62), residues: 79 loop : 0.78 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 70 HIS 0.004 0.001 HIS A 163 PHE 0.017 0.001 PHE A 35 TYR 0.019 0.001 TYR A 309 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7179 (mmtt) cc_final: 0.6257 (pttt) REVERT: A 121 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: A 175 VAL cc_start: 0.7929 (t) cc_final: 0.7607 (m) REVERT: A 205 ARG cc_start: 0.6808 (mtt180) cc_final: 0.6301 (mtm110) REVERT: A 207 LYS cc_start: 0.7284 (tptm) cc_final: 0.6893 (ttmt) REVERT: A 210 GLN cc_start: 0.8311 (pt0) cc_final: 0.8049 (pt0) REVERT: A 338 ASN cc_start: 0.6215 (p0) cc_final: 0.5678 (p0) REVERT: A 349 TRP cc_start: 0.6957 (p-90) cc_final: 0.6709 (p-90) outliers start: 13 outliers final: 7 residues processed: 44 average time/residue: 0.3012 time to fit residues: 16.1858 Evaluate side-chains 33 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 317 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6167 Z= 0.243 Angle : 0.508 4.520 8952 Z= 0.280 Chirality : 0.034 0.190 1070 Planarity : 0.004 0.043 648 Dihedral : 22.877 95.477 2373 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.57 % Allowed : 11.69 % Favored : 84.74 % 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: 2.26 (0.45), residues: 358 helix: 2.52 (0.38), residues: 175 sheet: 0.35 (0.64), residues: 73 loop : 0.76 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 70 HIS 0.004 0.001 HIS A 163 PHE 0.024 0.002 PHE A 35 TYR 0.021 0.002 TYR A 309 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7276 (mmtt) cc_final: 0.6273 (pttt) REVERT: A 121 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: A 205 ARG cc_start: 0.6779 (mtt180) cc_final: 0.6218 (mtm110) REVERT: A 210 GLN cc_start: 0.8257 (pt0) cc_final: 0.7975 (pt0) REVERT: A 278 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5303 (pt0) REVERT: A 330 LEU cc_start: 0.5787 (mp) cc_final: 0.5514 (mp) REVERT: A 338 ASN cc_start: 0.6514 (p0) cc_final: 0.5888 (p0) REVERT: A 349 TRP cc_start: 0.6897 (p-90) cc_final: 0.5895 (p-90) outliers start: 11 outliers final: 9 residues processed: 37 average time/residue: 0.2336 time to fit residues: 11.0851 Evaluate side-chains 35 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 12 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6167 Z= 0.318 Angle : 0.557 4.696 8952 Z= 0.304 Chirality : 0.037 0.226 1070 Planarity : 0.004 0.046 648 Dihedral : 22.934 96.313 2373 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.90 % Allowed : 12.66 % Favored : 83.44 % 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: 1.81 (0.45), residues: 358 helix: 2.16 (0.38), residues: 175 sheet: -0.08 (0.63), residues: 75 loop : 0.72 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 141 HIS 0.004 0.001 HIS A 163 PHE 0.025 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.003 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.6957 (tp) cc_final: 0.6675 (tt) REVERT: A 48 LYS cc_start: 0.7341 (mmtt) cc_final: 0.6229 (pttt) REVERT: A 108 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7592 (mtp85) REVERT: A 121 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: A 205 ARG cc_start: 0.6842 (mtt180) cc_final: 0.6253 (mtm110) REVERT: A 210 GLN cc_start: 0.8263 (pt0) cc_final: 0.8016 (pt0) REVERT: A 278 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5297 (pt0) REVERT: A 349 TRP cc_start: 0.6983 (p-90) cc_final: 0.5938 (p-90) outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.1981 time to fit residues: 11.1497 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6167 Z= 0.217 Angle : 0.486 4.469 8952 Z= 0.270 Chirality : 0.034 0.180 1070 Planarity : 0.004 0.046 648 Dihedral : 22.855 96.320 2373 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.87 % Allowed : 12.66 % Favored : 82.47 % 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: 1.94 (0.45), residues: 358 helix: 2.39 (0.38), residues: 175 sheet: 0.05 (0.64), residues: 73 loop : 0.50 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 141 HIS 0.004 0.001 HIS A 163 PHE 0.021 0.002 PHE A 35 TYR 0.021 0.002 TYR A 309 ARG 0.003 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.6831 (tt0) cc_final: 0.6447 (pt0) REVERT: A 48 LYS cc_start: 0.7315 (mmtt) cc_final: 0.6195 (pttt) REVERT: A 108 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7568 (mtp85) REVERT: A 121 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: A 176 GLU cc_start: 0.7626 (pt0) cc_final: 0.7376 (tm-30) REVERT: A 205 ARG cc_start: 0.6854 (mtt180) cc_final: 0.6229 (mtm110) REVERT: A 210 GLN cc_start: 0.8178 (pt0) cc_final: 0.7944 (pt0) REVERT: A 278 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.5085 (pt0) REVERT: A 329 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7229 (mm110) REVERT: A 349 TRP cc_start: 0.7021 (p-90) cc_final: 0.5784 (p-90) outliers start: 15 outliers final: 12 residues processed: 42 average time/residue: 0.2080 time to fit residues: 11.5456 Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6167 Z= 0.372 Angle : 0.601 4.823 8952 Z= 0.325 Chirality : 0.039 0.242 1070 Planarity : 0.005 0.049 648 Dihedral : 23.046 97.162 2373 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.55 % Allowed : 14.29 % Favored : 81.17 % 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: 1.37 (0.44), residues: 358 helix: 1.95 (0.38), residues: 175 sheet: -0.47 (0.62), residues: 75 loop : 0.39 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.005 0.002 HIS A 166 PHE 0.024 0.002 PHE A 35 TYR 0.025 0.002 TYR A 309 ARG 0.003 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.6981 (tp) cc_final: 0.6695 (tt) REVERT: A 48 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6240 (pttt) REVERT: A 108 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7521 (mtp85) REVERT: A 121 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: A 199 ILE cc_start: 0.7499 (mm) cc_final: 0.7237 (tt) REVERT: A 205 ARG cc_start: 0.6769 (mtt180) cc_final: 0.6202 (mtm110) REVERT: A 210 GLN cc_start: 0.8246 (pt0) cc_final: 0.8003 (pt0) REVERT: A 271 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: A 278 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5257 (pt0) REVERT: A 349 TRP cc_start: 0.7007 (p-90) cc_final: 0.5524 (p-90) outliers start: 14 outliers final: 9 residues processed: 45 average time/residue: 0.1952 time to fit residues: 11.7605 Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6167 Z= 0.160 Angle : 0.450 4.915 8952 Z= 0.250 Chirality : 0.032 0.149 1070 Planarity : 0.003 0.047 648 Dihedral : 22.836 95.655 2372 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.22 % Allowed : 14.29 % Favored : 81.49 % 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: 2.01 (0.46), residues: 358 helix: 2.54 (0.38), residues: 175 sheet: -0.11 (0.64), residues: 75 loop : 0.51 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 349 HIS 0.004 0.001 HIS A 279 PHE 0.016 0.001 PHE A 35 TYR 0.019 0.001 TYR A 309 ARG 0.002 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.6804 (mmtt) cc_final: 0.5769 (pttt) REVERT: A 108 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7392 (mtp85) REVERT: A 121 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: A 176 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7203 (mm-30) REVERT: A 205 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6155 (mtm110) REVERT: A 278 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.5009 (pt0) REVERT: A 349 TRP cc_start: 0.7004 (p-90) cc_final: 0.5676 (p-90) outliers start: 13 outliers final: 10 residues processed: 44 average time/residue: 0.1991 time to fit residues: 11.5294 Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 45 optimal weight: 40.0000 chunk 41 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 overall best weight: 6.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6167 Z= 0.360 Angle : 0.587 5.033 8952 Z= 0.318 Chirality : 0.038 0.234 1070 Planarity : 0.005 0.048 648 Dihedral : 23.017 96.751 2372 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 13.96 % Favored : 81.17 % 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: 1.41 (0.45), residues: 358 helix: 2.06 (0.37), residues: 175 sheet: -0.54 (0.62), residues: 75 loop : 0.33 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.005 0.002 HIS A 166 PHE 0.023 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.5741 (OUTLIER) cc_final: 0.5509 (p0) REVERT: A 48 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6400 (pttt) REVERT: A 93 PHE cc_start: 0.8101 (t80) cc_final: 0.7770 (t80) REVERT: A 108 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7440 (mtp85) REVERT: A 121 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: A 176 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7255 (mm-30) REVERT: A 199 ILE cc_start: 0.7495 (mm) cc_final: 0.7244 (tt) REVERT: A 205 ARG cc_start: 0.6625 (mtt180) cc_final: 0.6084 (mtm110) REVERT: A 271 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: A 278 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5245 (pt0) REVERT: A 349 TRP cc_start: 0.7014 (p-90) cc_final: 0.5543 (p-90) outliers start: 15 outliers final: 10 residues processed: 43 average time/residue: 0.1922 time to fit residues: 10.9229 Evaluate side-chains 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6167 Z= 0.418 Angle : 0.625 5.083 8952 Z= 0.336 Chirality : 0.040 0.241 1070 Planarity : 0.005 0.048 648 Dihedral : 23.066 96.725 2372 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.52 % Allowed : 13.64 % Favored : 80.84 % 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: 0.91 (0.44), residues: 358 helix: 1.76 (0.37), residues: 175 sheet: -1.00 (0.59), residues: 75 loop : 0.07 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.006 0.002 HIS A 166 PHE 0.027 0.003 PHE A 35 TYR 0.025 0.003 TYR A 309 ARG 0.004 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.6120 (OUTLIER) cc_final: 0.5886 (p0) REVERT: A 48 LYS cc_start: 0.7266 (mmtt) cc_final: 0.6423 (pttt) REVERT: A 93 PHE cc_start: 0.8193 (t80) cc_final: 0.7663 (t80) REVERT: A 108 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7439 (mtp85) REVERT: A 121 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: A 176 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7234 (mm-30) REVERT: A 205 ARG cc_start: 0.6685 (mtt180) cc_final: 0.6207 (mtm110) REVERT: A 271 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: A 278 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5271 (pt0) REVERT: A 349 TRP cc_start: 0.6913 (p-90) cc_final: 0.5423 (p-90) outliers start: 17 outliers final: 10 residues processed: 45 average time/residue: 0.1933 time to fit residues: 11.6945 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6167 Z= 0.322 Angle : 0.564 5.271 8952 Z= 0.305 Chirality : 0.037 0.219 1070 Planarity : 0.005 0.048 648 Dihedral : 23.052 96.812 2372 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.55 % Allowed : 13.96 % Favored : 81.49 % 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: 0.95 (0.44), residues: 358 helix: 1.91 (0.38), residues: 175 sheet: -1.08 (0.58), residues: 75 loop : -0.05 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.005 0.001 HIS A 163 PHE 0.024 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.003 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.5730 (OUTLIER) cc_final: 0.5500 (p0) REVERT: A 20 LEU cc_start: 0.7028 (tp) cc_final: 0.6749 (tt) REVERT: A 48 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6159 (pttt) REVERT: A 108 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7445 (mtp85) REVERT: A 121 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: A 176 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6848 (tm-30) REVERT: A 205 ARG cc_start: 0.6646 (mtt180) cc_final: 0.6133 (mtm110) REVERT: A 271 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: A 278 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5158 (pt0) REVERT: A 349 TRP cc_start: 0.7019 (p-90) cc_final: 0.5564 (p-90) outliers start: 14 outliers final: 10 residues processed: 44 average time/residue: 0.2975 time to fit residues: 17.3433 Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** 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 = 0.4091 r_free = 0.4091 target = 0.173207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137059 restraints weight = 8542.405| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.63 r_work: 0.3451 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6167 Z= 0.263 Angle : 0.525 5.420 8952 Z= 0.286 Chirality : 0.035 0.201 1070 Planarity : 0.004 0.048 648 Dihedral : 22.998 96.260 2372 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.19 % Allowed : 13.31 % Favored : 81.49 % 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: 1.12 (0.45), residues: 358 helix: 2.11 (0.38), residues: 175 sheet: -1.01 (0.59), residues: 75 loop : -0.07 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 141 HIS 0.004 0.002 HIS A 163 PHE 0.023 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.002 0.000 ARG A 23 =============================================================================== Job complete usr+sys time: 1052.96 seconds wall clock time: 20 minutes 27.42 seconds (1227.42 seconds total)