Starting phenix.real_space_refine on Mon Jan 13 18:42:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xct_38254/01_2025/8xct_38254_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xct_38254/01_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_38254/01_2025/8xct_38254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xct_38254/01_2025/8xct_38254.map" model { file = "/net/cci-nas-00/data/ceres_data/8xct_38254/01_2025/8xct_38254_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xct_38254/01_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-5571/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: 4.28, per 1000 atoms: 1.27 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: 0.88 Conformation dependent library (CDL) restraints added in 737.6 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: 0.95 Time building geometry restraints manager: 1.02 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: 0.710 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.130 Find NCS groups from input model: 0.030 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- 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 : 0.524 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: 1.4606 time to fit residues: 119.7415 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 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 = 0.090327 restraints weight = 8391.412| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.34 r_work: 0.2696 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 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 : 0.385 Fit side-chains REVERT: A 277 THR cc_start: 0.8298 (m) cc_final: 0.7915 (p) REVERT: A 283 GLU cc_start: 0.7809 (tt0) cc_final: 0.7555 (mt-10) REVERT: A 303 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8329 (pt0) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 1.3957 time to fit residues: 107.4324 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 : 0.494 ------------------------------------------------------------------------------- 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: 0.0270 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.116706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.093954 restraints weight = 6302.427| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.01 r_work: 0.2752 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3410 Z= 0.151 Angle : 0.505 10.570 4635 Z= 0.256 Chirality : 0.043 0.138 503 Planarity : 0.005 0.060 589 Dihedral : 7.509 117.567 468 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % 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: 1.76 (0.43), residues: 416 helix: 2.38 (0.35), residues: 212 sheet: -0.13 (0.70), residues: 67 loop : -0.02 (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 0.007 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 : 0.427 Fit side-chains REVERT: A 277 THR cc_start: 0.8303 (m) cc_final: 0.7893 (p) REVERT: A 303 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: A 366 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7773 (mt-10) outliers start: 7 outliers final: 1 residues processed: 66 average time/residue: 1.3902 time to fit residues: 94.3012 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 : 0.406 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.091537 restraints weight = 14156.623| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.03 r_work: 0.2728 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 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 = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3410 Z= 0.171 Angle : 0.500 11.540 4635 Z= 0.254 Chirality : 0.043 0.137 503 Planarity : 0.005 0.052 589 Dihedral : 6.924 99.521 468 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.61 % Favored : 96.14 % Rotamer: Outliers : 2.65 % Allowed : 14.12 % 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: 1.74 (0.43), residues: 416 helix: 2.36 (0.35), residues: 211 sheet: 0.11 (0.66), residues: 72 loop : -0.17 (0.57), residues: 133 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 0.010 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 246 *********************** 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 75 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.385 Fit side-chains REVERT: A 277 THR cc_start: 0.8328 (m) cc_final: 0.7910 (p) REVERT: A 303 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: A 366 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7690 (mt-10) outliers start: 9 outliers final: 2 residues processed: 67 average time/residue: 1.2984 time to fit residues: 89.4664 Evaluate side-chains 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS 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: 1.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.086579 restraints weight = 10534.842| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.62 r_work: 0.2558 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3410 Z= 0.278 Angle : 0.547 12.607 4635 Z= 0.280 Chirality : 0.045 0.157 503 Planarity : 0.005 0.051 589 Dihedral : 6.711 72.917 468 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 1.76 % Allowed : 14.71 % Favored : 83.53 % 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: 1.55 (0.43), residues: 416 helix: 2.21 (0.35), residues: 210 sheet: -0.04 (0.66), 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 0.006 0.001 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.002 0.000 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.395 Fit side-chains REVERT: A 303 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8346 (pt0) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 1.4357 time to fit residues: 88.4713 Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.112740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.088803 restraints weight = 10520.974| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.66 r_work: 0.2641 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3410 Z= 0.245 Angle : 0.530 11.200 4635 Z= 0.273 Chirality : 0.044 0.146 503 Planarity : 0.005 0.049 589 Dihedral : 6.184 63.758 468 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.41 % Favored : 97.35 % Rotamer: Outliers : 2.94 % Allowed : 13.24 % Favored : 83.82 % 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: 1.54 (0.42), residues: 416 helix: 2.35 (0.35), residues: 205 sheet: -0.01 (0.74), residues: 58 loop : -0.38 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.012 0.002 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** 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 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.424 Fit side-chains REVERT: A 303 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: A 366 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7881 (mt-10) outliers start: 10 outliers final: 2 residues processed: 64 average time/residue: 1.3926 time to fit residues: 91.6325 Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.115084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.092636 restraints weight = 6322.005| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.02 r_work: 0.2716 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 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 = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3410 Z= 0.183 Angle : 0.491 8.288 4635 Z= 0.254 Chirality : 0.043 0.130 503 Planarity : 0.005 0.046 589 Dihedral : 5.356 50.356 468 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 1.76 % Allowed : 13.82 % Favored : 84.41 % 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: 1.68 (0.43), residues: 416 helix: 2.28 (0.35), residues: 211 sheet: 0.06 (0.67), residues: 72 loop : -0.11 (0.58), residues: 133 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 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** 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 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.381 Fit side-chains REVERT: A 41 SER cc_start: 0.9054 (m) cc_final: 0.8700 (p) REVERT: A 303 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8361 (pt0) outliers start: 6 outliers final: 0 residues processed: 64 average time/residue: 1.2770 time to fit residues: 84.0734 Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.111701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.088919 restraints weight = 6744.341| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.08 r_work: 0.2591 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3410 Z= 0.278 Angle : 0.535 8.260 4635 Z= 0.278 Chirality : 0.045 0.147 503 Planarity : 0.005 0.046 589 Dihedral : 4.996 44.554 465 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 1.18 % Allowed : 15.59 % 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: 1.54 (0.42), residues: 416 helix: 2.36 (0.35), residues: 205 sheet: 0.00 (0.74), residues: 58 loop : -0.39 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 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: 4 poor density : 62 time to evaluate : 0.425 Fit side-chains REVERT: A 41 SER cc_start: 0.8989 (m) cc_final: 0.8567 (p) REVERT: A 303 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8424 (pt0) outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 1.3566 time to fit residues: 86.5304 Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.114435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.090609 restraints weight = 10444.380| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.61 r_work: 0.2610 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 0.049 3410 Z= 0.193 Angle : 0.502 8.006 4635 Z= 0.261 Chirality : 0.043 0.129 503 Planarity : 0.005 0.046 589 Dihedral : 4.811 41.180 465 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.77 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: 1.61 (0.43), residues: 416 helix: 2.23 (0.35), residues: 211 sheet: -0.00 (0.66), residues: 72 loop : -0.14 (0.58), residues: 133 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 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.002 0.000 ARG A 246 *********************** 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 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.381 Fit side-chains REVERT: A 41 SER cc_start: 0.9007 (m) cc_final: 0.8602 (p) REVERT: A 246 ARG cc_start: 0.7535 (mmt-90) cc_final: 0.6831 (mpt180) REVERT: A 303 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: A 366 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7907 (tt0) outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 1.3743 time to fit residues: 86.1859 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 : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 overall best weight: 2.3964 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.110194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.087184 restraints weight = 6704.456| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.10 r_work: 0.2593 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.067 | | 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: 0.8764 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3410 Z= 0.290 Angle : 0.542 8.052 4635 Z= 0.284 Chirality : 0.045 0.150 503 Planarity : 0.005 0.046 589 Dihedral : 4.949 42.526 465 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 15.00 % Favored : 83.53 % 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: 1.47 (0.42), residues: 416 helix: 2.32 (0.35), residues: 205 sheet: -0.16 (0.73), residues: 58 loop : -0.40 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.006 0.001 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.003 0.000 ARG A 246 ********************** 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 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.381 Fit side-chains REVERT: A 41 SER cc_start: 0.9013 (m) cc_final: 0.8613 (p) REVERT: A 246 ARG cc_start: 0.7606 (mmt-90) cc_final: 0.7143 (mpt180) REVERT: A 303 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: A 366 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7956 (tt0) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 1.3840 time to fit residues: 83.9694 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.0570 chunk 35 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.117289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.092684 restraints weight = 14072.041| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.02 r_work: 0.2682 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3410 Z= 0.156 Angle : 0.504 8.075 4635 Z= 0.261 Chirality : 0.042 0.126 503 Planarity : 0.005 0.047 589 Dihedral : 4.663 39.671 465 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % 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: 1.65 (0.43), residues: 416 helix: 2.28 (0.35), residues: 211 sheet: 0.01 (0.66), residues: 72 loop : -0.16 (0.58), 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 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 408 ARG 0.004 0.000 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3091.51 seconds wall clock time: 55 minutes 24.73 seconds (3324.73 seconds total)