Starting phenix.real_space_refine on Wed Mar 5 21:02:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcw_38257/03_2025/8xcw_38257_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcw_38257/03_2025/8xcw_38257.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/8xcw_38257/03_2025/8xcw_38257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcw_38257/03_2025/8xcw_38257.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcw_38257/03_2025/8xcw_38257_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcw_38257/03_2025/8xcw_38257_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 2118 2.51 5 N 564 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 3347 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3272 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3261 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 416, 3261 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3320 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 75 Unusual residues: {'AKG': 1, 'NDP': 1} Classifications: {'undetermined': 2, 'water': 17} Link IDs: {None: 18} Time building chain proxies: 4.36, per 1000 atoms: 1.30 Number of scatterers: 3347 At special positions: 0 Unit cell: (67.68, 72.944, 72.192, 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 648 8.00 N 564 7.00 C 2118 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: 0.81 Conformation dependent library (CDL) restraints added in 764.5 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 56.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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: 3.521A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.775A 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: 3.801A 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 305 through 309 Processing helix chain 'A' and resid 323 through 334 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 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.687A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.353A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 536 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: 0.94 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1052 1.34 - 1.45: 440 1.45 - 1.57: 1887 1.57 - 1.69: 3 1.69 - 1.80: 27 Bond restraints: 3409 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.613 -0.089 1.26e-02 6.30e+03 5.04e+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 4.97e+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 4.83e+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=" C1 AKG A 501 " pdb=" C2 AKG A 501 " ideal model delta sigma weight residual 1.559 1.459 0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 3404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 4592 4.42 - 8.84: 24 8.84 - 13.27: 13 13.27 - 17.69: 4 17.69 - 22.11: 1 Bond angle restraints: 4634 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 105.41 127.52 -22.11 2.71e+00 1.37e-01 6.68e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.14 -15.30 1.91e+00 2.73e-01 6.39e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.47 -14.73 1.95e+00 2.62e-01 5.69e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.54 7.92 1.17e+00 7.36e-01 4.61e+01 angle pdb=" N TRP A 89 " pdb=" CA BTRP A 89 " pdb=" C TRP A 89 " ideal model delta sigma weight residual 111.14 104.62 6.52 1.08e+00 8.57e-01 3.64e+01 ... (remaining 4629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.02: 1872 25.02 - 50.04: 123 50.04 - 75.05: 16 75.05 - 100.07: 3 100.07 - 125.09: 1 Dihedral angle restraints: 2015 sinusoidal: 822 harmonic: 1193 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 49.95 125.09 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CB GLU A 8 " pdb=" CG GLU A 8 " pdb=" CD GLU A 8 " pdb=" OE1 GLU A 8 " ideal model delta sinusoidal sigma weight residual 0.00 -88.42 88.42 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" N SER A 351 " pdb=" CA SER A 351 " pdb=" CB SER A 351 " pdb=" OG SER A 351 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 443 0.078 - 0.157: 51 0.157 - 0.235: 1 0.235 - 0.313: 4 0.313 - 0.392: 3 Chirality restraints: 502 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 -0.39 2.00e-01 2.50e+01 3.84e+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 3.24e+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 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 499 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.103 2.00e-02 2.50e+03 1.98e-01 3.90e+02 pdb=" C5N NDP A 500 " 0.255 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.261 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=" CA ASP A 244 " -0.018 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" C ASP A 244 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP A 244 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 245 " -0.019 2.00e-02 2.50e+03 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1198 2.87 - 3.38: 3282 3.38 - 3.89: 5935 3.89 - 4.39: 6843 4.39 - 4.90: 11313 Nonbonded interactions: 28571 Sorted by model distance: nonbonded pdb=" NZ LYS A 69 " pdb=" OG1 THR A 175 " model vdw 2.363 3.120 nonbonded pdb=" O ASN A 344 " pdb=" OD1 ASN A 344 " model vdw 2.395 3.040 nonbonded pdb=" O PRO A 34 " pdb=" O HOH A 601 " model vdw 2.452 3.040 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.453 3.040 nonbonded pdb=" O PRO A 76 " pdb=" O HOH A 602 " model vdw 2.458 3.040 ... (remaining 28566 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: 0.680 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.120 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:12.600 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: 0.8619 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 3409 Z= 0.619 Angle : 1.103 22.112 4634 Z= 0.570 Chirality : 0.058 0.392 502 Planarity : 0.010 0.198 591 Dihedral : 16.211 125.090 1255 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.54 % Allowed : 2.95 % Favored : 93.51 % 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 (0.43), residues: 415 helix: 2.03 (0.35), residues: 211 sheet: -0.53 (0.79), residues: 48 loop : -0.27 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 263 HIS 0.001 0.000 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 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.375 Fit side-chains REVERT: A 310 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8743 (mttp) REVERT: A 371 GLU cc_start: 0.7470 (tp30) cc_final: 0.7229 (mm-30) outliers start: 10 outliers final: 2 residues processed: 71 average time/residue: 1.7048 time to fit residues: 123.5810 Evaluate side-chains 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 351 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 234 GLN A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.083992 restraints weight = 8591.064| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.20 r_work: 0.2680 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3409 Z= 0.164 Angle : 0.468 4.955 4634 Z= 0.249 Chirality : 0.042 0.129 502 Planarity : 0.004 0.043 591 Dihedral : 8.519 123.898 475 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.77 % Allowed : 13.27 % Favored : 84.96 % 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: 1.80 (0.43), residues: 415 helix: 2.50 (0.35), residues: 212 sheet: -0.04 (0.80), residues: 50 loop : -0.22 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.002 0.001 HIS A 61 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.006 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.405 Fit side-chains REVERT: A 222 ASN cc_start: 0.8915 (t0) cc_final: 0.8654 (t0) REVERT: A 332 GLU cc_start: 0.9044 (tp30) cc_final: 0.8830 (tp30) REVERT: A 371 GLU cc_start: 0.8617 (tp30) cc_final: 0.8357 (mm-30) REVERT: A 382 TRP cc_start: 0.8899 (m100) cc_final: 0.8601 (m100) outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 1.6512 time to fit residues: 91.3806 Evaluate side-chains 49 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.081950 restraints weight = 6675.230| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 1.94 r_work: 0.2595 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3409 Z= 0.202 Angle : 0.469 5.669 4634 Z= 0.248 Chirality : 0.043 0.131 502 Planarity : 0.004 0.040 591 Dihedral : 7.697 121.769 468 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.77 % Allowed : 14.45 % Favored : 83.78 % 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: 1.96 (0.43), residues: 415 helix: 2.57 (0.35), residues: 212 sheet: 0.14 (0.68), residues: 70 loop : -0.11 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.001 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.366 Fit side-chains REVERT: A 371 GLU cc_start: 0.8642 (tp30) cc_final: 0.8439 (mm-30) outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 1.6778 time to fit residues: 89.2325 Evaluate side-chains 47 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.082564 restraints weight = 7092.628| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.03 r_work: 0.2619 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3409 Z= 0.167 Angle : 0.452 5.071 4634 Z= 0.240 Chirality : 0.042 0.126 502 Planarity : 0.004 0.042 591 Dihedral : 7.436 121.665 468 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.18 % Allowed : 14.75 % Favored : 84.07 % 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: 1.89 (0.43), residues: 415 helix: 2.61 (0.35), residues: 212 sheet: -0.23 (0.72), residues: 62 loop : -0.12 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.001 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.007 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.347 Fit side-chains REVERT: A 13 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8224 (tm-30) REVERT: A 191 THR cc_start: 0.9210 (m) cc_final: 0.8970 (t) REVERT: A 332 GLU cc_start: 0.9015 (tp30) cc_final: 0.8765 (tp30) REVERT: A 382 TRP cc_start: 0.8929 (m100) cc_final: 0.8624 (m100) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 1.4847 time to fit residues: 82.2038 Evaluate side-chains 49 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.081712 restraints weight = 6758.453| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 1.97 r_work: 0.2629 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3409 Z= 0.197 Angle : 0.472 5.134 4634 Z= 0.250 Chirality : 0.042 0.126 502 Planarity : 0.004 0.043 591 Dihedral : 7.382 119.941 468 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 16.22 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.43), residues: 415 helix: 2.61 (0.35), residues: 212 sheet: 0.16 (0.67), residues: 70 loop : -0.14 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.001 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.005 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.357 Fit side-chains REVERT: A 191 THR cc_start: 0.9227 (m) cc_final: 0.8972 (t) REVERT: A 332 GLU cc_start: 0.9045 (tp30) cc_final: 0.8806 (tp30) REVERT: A 382 TRP cc_start: 0.8956 (m100) cc_final: 0.8612 (m100) outliers start: 3 outliers final: 0 residues processed: 54 average time/residue: 1.4501 time to fit residues: 80.3400 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.082111 restraints weight = 12290.421| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.65 r_work: 0.2628 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3409 Z= 0.159 Angle : 0.478 5.215 4634 Z= 0.253 Chirality : 0.042 0.127 502 Planarity : 0.005 0.053 591 Dihedral : 7.234 116.687 468 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.18 % Allowed : 16.81 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.43), residues: 415 helix: 2.67 (0.35), residues: 212 sheet: 0.19 (0.67), residues: 70 loop : -0.14 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.001 0.000 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.013 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 191 THR cc_start: 0.9209 (m) cc_final: 0.8975 (t) REVERT: A 332 GLU cc_start: 0.9119 (tp30) cc_final: 0.8886 (tp30) REVERT: A 370 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8108 (ttm170) REVERT: A 382 TRP cc_start: 0.8890 (m100) cc_final: 0.8623 (m100) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 1.4470 time to fit residues: 80.1513 Evaluate side-chains 49 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.081468 restraints weight = 12080.428| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.64 r_work: 0.2609 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3409 Z= 0.165 Angle : 0.467 5.063 4634 Z= 0.248 Chirality : 0.042 0.127 502 Planarity : 0.004 0.043 591 Dihedral : 6.944 107.912 468 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 16.81 % Favored : 81.12 % 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: 1.89 (0.43), residues: 415 helix: 2.63 (0.35), residues: 213 sheet: -0.20 (0.72), residues: 62 loop : -0.20 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.006 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.395 Fit side-chains REVERT: A 12 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7136 (mttt) REVERT: A 332 GLU cc_start: 0.9095 (tp30) cc_final: 0.8854 (tp30) REVERT: A 370 ARG cc_start: 0.8548 (ttm-80) cc_final: 0.8122 (ttm170) REVERT: A 371 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8494 (mm-30) REVERT: A 375 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.9014 (mptt) REVERT: A 382 TRP cc_start: 0.8902 (m100) cc_final: 0.8617 (m100) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 1.5018 time to fit residues: 84.7078 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.082141 restraints weight = 7135.684| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.02 r_work: 0.2634 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2452 r_free = 0.2452 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2452 r_free = 0.2452 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3409 Z= 0.190 Angle : 0.484 5.343 4634 Z= 0.256 Chirality : 0.042 0.127 502 Planarity : 0.005 0.063 591 Dihedral : 6.666 95.040 468 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.36 % Allowed : 17.11 % Favored : 80.53 % 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: 1.97 (0.43), residues: 415 helix: 2.62 (0.35), residues: 213 sheet: 0.16 (0.67), residues: 70 loop : -0.22 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 263 HIS 0.001 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.015 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7130 (mttt) REVERT: A 332 GLU cc_start: 0.9048 (tp30) cc_final: 0.8816 (tp30) REVERT: A 370 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8049 (ttm170) REVERT: A 382 TRP cc_start: 0.8916 (m100) cc_final: 0.8612 (m100) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 1.5937 time to fit residues: 84.8555 Evaluate side-chains 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.082335 restraints weight = 12266.191| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.67 r_work: 0.2628 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3409 Z= 0.156 Angle : 0.469 4.953 4634 Z= 0.249 Chirality : 0.042 0.127 502 Planarity : 0.004 0.044 591 Dihedral : 6.259 79.682 468 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 17.99 % Favored : 80.53 % 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: 1.96 (0.43), residues: 415 helix: 2.63 (0.35), residues: 213 sheet: 0.13 (0.66), residues: 70 loop : -0.25 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.001 0.000 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.007 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 332 GLU cc_start: 0.9113 (tp30) cc_final: 0.8874 (tp30) REVERT: A 370 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8152 (ttm170) REVERT: A 382 TRP cc_start: 0.8872 (m100) cc_final: 0.8587 (m100) outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 1.4714 time to fit residues: 79.9882 Evaluate side-chains 48 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.0000 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.084282 restraints weight = 7125.006| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.04 r_work: 0.2690 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3409 Z= 0.154 Angle : 0.479 5.986 4634 Z= 0.254 Chirality : 0.041 0.128 502 Planarity : 0.005 0.059 591 Dihedral : 6.056 72.275 468 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.88 % Allowed : 18.29 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.43), residues: 415 helix: 2.63 (0.35), residues: 213 sheet: 0.43 (0.69), residues: 67 loop : -0.31 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 263 HIS 0.001 0.000 HIS A 394 PHE 0.008 0.001 PHE A 341 TYR 0.005 0.001 TYR A 363 ARG 0.016 0.001 ARG A 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 218 GLN cc_start: 0.9060 (tt0) cc_final: 0.8858 (tt0) REVERT: A 332 GLU cc_start: 0.9034 (tp30) cc_final: 0.8831 (tp30) REVERT: A 370 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8068 (ttm170) REVERT: A 382 TRP cc_start: 0.8837 (m100) cc_final: 0.8536 (m100) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 1.5941 time to fit residues: 78.4571 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.080402 restraints weight = 11106.585| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.54 r_work: 0.2584 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3409 Z= 0.220 Angle : 0.506 5.536 4634 Z= 0.270 Chirality : 0.043 0.142 502 Planarity : 0.004 0.043 591 Dihedral : 6.030 65.037 468 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.18 % Allowed : 17.99 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.43), residues: 415 helix: 2.63 (0.35), residues: 212 sheet: -0.27 (0.71), residues: 62 loop : -0.12 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 263 HIS 0.001 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.009 0.001 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.96 seconds wall clock time: 57 minutes 0.99 seconds (3420.99 seconds total)