Starting phenix.real_space_refine on Wed Mar 5 20:51:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xct_38254/03_2025/8xct_38254_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xct_38254/03_2025/8xct_38254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xct_38254/03_2025/8xct_38254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xct_38254/03_2025/8xct_38254.map" model { file = "/net/cci-nas-00/data/ceres_data/8xct_38254/03_2025/8xct_38254_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xct_38254/03_2025/8xct_38254_neut.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2120 2.51 5 N 566 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3358 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 417, 3271 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 417, 3271 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3330 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 76 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 28} Link IDs: {None: 28} Time building chain proxies: 4.39, per 1000 atoms: 1.31 Number of scatterers: 3358 At special positions: 0 Unit cell: (68.432, 74.448, 73.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 655 8.00 N 566 7.00 C 2120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 777.2 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 54.7% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.524A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.503A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.406A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1073 1.34 - 1.46: 560 1.46 - 1.57: 1747 1.57 - 1.69: 3 1.69 - 1.81: 27 Bond restraints: 3410 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.616 -0.093 1.29e-02 6.01e+03 5.19e+01 bond pdb=" O1N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.477 1.548 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.569 0.264 3.80e-02 6.93e+02 4.84e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.21e+01 bond pdb=" C6A NDP A 500 " pdb=" N1A NDP A 500 " ideal model delta sigma weight residual 1.368 1.251 0.117 2.90e-02 1.19e+03 1.62e+01 ... (remaining 3405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 4593 4.41 - 8.83: 24 8.83 - 13.24: 13 13.24 - 17.65: 4 17.65 - 22.07: 1 Bond angle restraints: 4635 Sorted by residual: angle pdb=" C1D NDP A 500 " pdb=" O4D NDP A 500 " pdb=" C4D NDP A 500 " ideal model delta sigma weight residual 105.41 127.48 -22.07 2.71e+00 1.37e-01 6.65e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.21 -15.37 1.91e+00 2.73e-01 6.45e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.38 -14.64 1.95e+00 2.62e-01 5.61e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.48 7.98 1.17e+00 7.36e-01 4.68e+01 angle pdb=" O2X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.33 108.94 8.39 1.48e+00 4.57e-01 3.22e+01 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 1872 23.85 - 47.69: 118 47.69 - 71.54: 24 71.54 - 95.38: 4 95.38 - 119.23: 1 Dihedral angle restraints: 2019 sinusoidal: 823 harmonic: 1196 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 55.81 119.23 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " pdb=" CG ASP A 256 " pdb=" OD1 ASP A 256 " ideal model delta sinusoidal sigma weight residual -30.00 -86.92 56.92 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA GLU A 366 " pdb=" CB GLU A 366 " pdb=" CG GLU A 366 " pdb=" CD GLU A 366 " ideal model delta sinusoidal sigma weight residual -180.00 -121.79 -58.21 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 441 0.079 - 0.158: 53 0.158 - 0.237: 3 0.237 - 0.316: 3 0.316 - 0.395: 3 Chirality restraints: 503 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.35 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 500 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.104 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C5N NDP A 500 " 0.256 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.262 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.059 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C3N NDP A 500 " 0.166 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " -0.038 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.106 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 144 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.050 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 859 2.80 - 3.33: 3195 3.33 - 3.85: 5729 3.85 - 4.38: 6963 4.38 - 4.90: 11740 Nonbonded interactions: 28486 Sorted by model distance: nonbonded pdb=" OE2 GLU A 114 " pdb=" O HOH A 601 " model vdw 2.278 3.040 nonbonded pdb=" NE ARG A 73 " pdb=" OE2 GLU A 78 " model vdw 2.476 3.120 nonbonded pdb=" O VAL A 348 " pdb=" OG SER A 351 " model vdw 2.493 3.040 nonbonded pdb=" OD2 ASP A 47 " pdb=" OG SER A 116 " model vdw 2.517 3.040 nonbonded pdb=" OE1 GLN A 357 " pdb=" O HOH A 602 " model vdw 2.518 3.040 ... (remaining 28481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.200 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.040 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 : 0.009 0.264 3410 Z= 0.650 Angle : 1.090 22.067 4635 Z= 0.555 Chirality : 0.058 0.395 503 Planarity : 0.011 0.198 589 Dihedral : 16.215 119.230 1257 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.00 % Allowed : 0.88 % Favored : 94.12 % 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: 1.25 (0.42), residues: 416 helix: 2.05 (0.35), residues: 211 sheet: -0.28 (0.69), residues: 66 loop : -0.46 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.001 0.000 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.349 Fit side-chains REVERT: A 244 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6327 (p0) REVERT: A 308 ASN cc_start: 0.7814 (m-40) cc_final: 0.7589 (m-40) outliers start: 17 outliers final: 3 residues processed: 80 average time/residue: 1.3653 time to fit residues: 111.9532 Evaluate side-chains 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 370 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.090326 restraints weight = 8391.412| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.34 r_work: 0.2709 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3410 Z= 0.227 Angle : 0.518 4.579 4635 Z= 0.272 Chirality : 0.044 0.167 503 Planarity : 0.005 0.073 589 Dihedral : 8.428 123.816 477 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 10.59 % Favored : 87.35 % 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: 1.64 (0.43), residues: 416 helix: 2.28 (0.35), residues: 213 sheet: -0.40 (0.69), residues: 68 loop : 0.04 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.395 Fit side-chains REVERT: A 277 THR cc_start: 0.8302 (m) cc_final: 0.7921 (p) REVERT: A 283 GLU cc_start: 0.7812 (tt0) cc_final: 0.7559 (mt-10) REVERT: A 303 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8328 (pt0) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 1.4636 time to fit residues: 112.7615 Evaluate side-chains 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 379 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.0030 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.092339 restraints weight = 6313.533| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.01 r_work: 0.2763 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3410 Z= 0.177 Angle : 0.511 10.000 4635 Z= 0.260 Chirality : 0.043 0.145 503 Planarity : 0.005 0.060 589 Dihedral : 7.571 116.978 468 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 14.71 % Favored : 83.24 % 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: 1.71 (0.43), residues: 416 helix: 2.34 (0.35), residues: 212 sheet: -0.19 (0.70), residues: 67 loop : -0.03 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.398 Fit side-chains REVERT: A 277 THR cc_start: 0.8371 (m) cc_final: 0.7954 (p) REVERT: A 303 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: A 366 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7842 (mt-10) outliers start: 7 outliers final: 1 residues processed: 66 average time/residue: 1.3980 time to fit residues: 94.9841 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.088291 restraints weight = 14184.355| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.02 r_work: 0.2641 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3410 Z= 0.229 Angle : 0.528 12.029 4635 Z= 0.271 Chirality : 0.044 0.149 503 Planarity : 0.005 0.055 589 Dihedral : 7.121 95.869 468 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.47 % Allowed : 15.29 % Favored : 83.24 % 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: 1.63 (0.43), residues: 416 helix: 2.31 (0.35), residues: 210 sheet: -0.03 (0.67), residues: 72 loop : -0.21 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.012 0.002 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.358 Fit side-chains REVERT: A 303 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8299 (pt0) outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 1.3457 time to fit residues: 85.7662 Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.083487 restraints weight = 10612.125| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.62 r_work: 0.2578 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 3410 Z= 0.503 Angle : 0.626 12.386 4635 Z= 0.327 Chirality : 0.049 0.196 503 Planarity : 0.006 0.053 589 Dihedral : 7.093 71.502 468 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 3.82 % Allowed : 12.94 % Favored : 83.24 % 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: 1.17 (0.41), residues: 416 helix: 2.03 (0.34), residues: 205 sheet: -0.21 (0.74), residues: 58 loop : -0.52 (0.50), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 382 HIS 0.008 0.002 HIS A 388 PHE 0.019 0.003 PHE A 341 TYR 0.014 0.002 TYR A 363 ARG 0.002 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.372 Fit side-chains REVERT: A 8 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7825 (pt0) REVERT: A 303 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8466 (pt0) outliers start: 13 outliers final: 4 residues processed: 63 average time/residue: 1.3144 time to fit residues: 85.0551 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.090557 restraints weight = 10520.022| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.62 r_work: 0.2687 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3410 Z= 0.176 Angle : 0.517 11.924 4635 Z= 0.265 Chirality : 0.043 0.129 503 Planarity : 0.005 0.049 589 Dihedral : 6.256 62.098 468 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.17 % Favored : 97.59 % Rotamer: Outliers : 2.35 % Allowed : 14.41 % Favored : 83.24 % 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: 1.52 (0.42), residues: 416 helix: 2.19 (0.34), residues: 211 sheet: -0.13 (0.66), residues: 72 loop : -0.20 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.373 Fit side-chains REVERT: A 41 SER cc_start: 0.9058 (m) cc_final: 0.8673 (p) REVERT: A 286 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: A 303 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: A 366 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7858 (mt-10) outliers start: 8 outliers final: 0 residues processed: 62 average time/residue: 1.3009 time to fit residues: 82.9678 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.094480 restraints weight = 6300.617| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.00 r_work: 0.2832 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 3410 Z= 0.164 Angle : 0.500 7.420 4635 Z= 0.255 Chirality : 0.042 0.126 503 Planarity : 0.005 0.046 589 Dihedral : 5.272 43.692 468 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 15.59 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.43), residues: 416 helix: 2.33 (0.35), residues: 211 sheet: -0.05 (0.65), residues: 73 loop : -0.07 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.404 Fit side-chains REVERT: A 41 SER cc_start: 0.9040 (m) cc_final: 0.8738 (p) REVERT: A 303 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8398 (pt0) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 1.3200 time to fit residues: 88.2543 Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.089589 restraints weight = 6735.400| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.10 r_work: 0.2717 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3410 Z= 0.271 Angle : 0.526 8.052 4635 Z= 0.271 Chirality : 0.044 0.147 503 Planarity : 0.005 0.046 589 Dihedral : 4.895 42.852 465 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.76 % Allowed : 15.00 % Favored : 83.24 % 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: 1.56 (0.43), residues: 416 helix: 2.23 (0.35), residues: 210 sheet: -0.12 (0.66), residues: 72 loop : -0.15 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.013 0.002 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.382 Fit side-chains REVERT: A 41 SER cc_start: 0.9053 (m) cc_final: 0.8709 (p) REVERT: A 246 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7660 (mpt180) REVERT: A 286 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: A 303 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8438 (pt0) outliers start: 6 outliers final: 0 residues processed: 61 average time/residue: 1.3030 time to fit residues: 81.6815 Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.091692 restraints weight = 10451.761| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.63 r_work: 0.2625 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3410 Z= 0.176 Angle : 0.504 7.745 4635 Z= 0.261 Chirality : 0.042 0.124 503 Planarity : 0.005 0.046 589 Dihedral : 4.655 40.600 465 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.47 % Allowed : 15.88 % Favored : 82.65 % 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: 1.67 (0.43), residues: 416 helix: 2.29 (0.35), residues: 211 sheet: -0.08 (0.65), residues: 73 loop : -0.06 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.380 Fit side-chains REVERT: A 41 SER cc_start: 0.9022 (m) cc_final: 0.8670 (p) REVERT: A 246 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7528 (mpt180) REVERT: A 286 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: A 303 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8418 (pt0) outliers start: 5 outliers final: 1 residues processed: 63 average time/residue: 1.2542 time to fit residues: 81.3360 Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.085764 restraints weight = 6737.543| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.11 r_work: 0.2698 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 3410 Z= 0.460 Angle : 0.606 8.050 4635 Z= 0.317 Chirality : 0.048 0.180 503 Planarity : 0.006 0.047 589 Dihedral : 5.181 44.603 465 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 1.18 % Allowed : 15.88 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.42), residues: 416 helix: 2.16 (0.35), residues: 205 sheet: -0.38 (0.73), residues: 58 loop : -0.43 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 382 HIS 0.007 0.002 HIS A 388 PHE 0.018 0.002 PHE A 341 TYR 0.013 0.002 TYR A 363 ARG 0.003 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.513 Fit side-chains REVERT: A 246 ARG cc_start: 0.8057 (mmt180) cc_final: 0.7681 (mpt180) REVERT: A 286 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: A 303 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8543 (pt0) outliers start: 4 outliers final: 0 residues processed: 57 average time/residue: 1.6055 time to fit residues: 94.0927 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.087889 restraints weight = 14197.293| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.00 r_work: 0.2687 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3410 Z= 0.210 Angle : 0.512 7.773 4635 Z= 0.268 Chirality : 0.043 0.133 503 Planarity : 0.005 0.046 589 Dihedral : 4.831 41.242 465 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.41 % Favored : 97.35 % Rotamer: Outliers : 0.88 % Allowed : 16.47 % Favored : 82.65 % 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 (0.43), residues: 416 helix: 2.14 (0.35), residues: 211 sheet: -0.28 (0.65), residues: 73 loop : -0.12 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.30 seconds wall clock time: 54 minutes 57.61 seconds (3297.61 seconds total)