Starting phenix.real_space_refine on Wed Sep 17 03:56:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xct_38254/09_2025/8xct_38254_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xct_38254/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xct_38254/09_2025/8xct_38254_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xct_38254/09_2025/8xct_38254_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xct_38254/09_2025/8xct_38254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xct_38254/09_2025/8xct_38254.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.36, per 1000 atoms: 0.41 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: 0.30 Conformation dependent library (CDL) restraints added in 213.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.13 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: 0.47 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1073 1.34 - 1.46: 560 1.46 - 1.57: 1747 1.57 - 1.69: 3 1.69 - 1.81: 27 Bond restraints: 3410 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.616 -0.093 1.29e-02 6.01e+03 5.19e+01 bond pdb=" O1N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.477 1.548 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.569 0.264 3.80e-02 6.93e+02 4.84e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.21e+01 bond pdb=" C6A NDP A 500 " pdb=" N1A NDP A 500 " ideal model delta sigma weight residual 1.368 1.251 0.117 2.90e-02 1.19e+03 1.62e+01 ... (remaining 3405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 4593 4.41 - 8.83: 24 8.83 - 13.24: 13 13.24 - 17.65: 4 17.65 - 22.07: 1 Bond angle restraints: 4635 Sorted by residual: angle pdb=" C1D NDP A 500 " pdb=" O4D NDP A 500 " pdb=" C4D NDP A 500 " ideal model delta sigma weight residual 105.41 127.48 -22.07 2.71e+00 1.37e-01 6.65e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.21 -15.37 1.91e+00 2.73e-01 6.45e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.38 -14.64 1.95e+00 2.62e-01 5.61e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.48 7.98 1.17e+00 7.36e-01 4.68e+01 angle pdb=" O2X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.33 108.94 8.39 1.48e+00 4.57e-01 3.22e+01 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 1872 23.85 - 47.69: 118 47.69 - 71.54: 24 71.54 - 95.38: 4 95.38 - 119.23: 1 Dihedral angle restraints: 2019 sinusoidal: 823 harmonic: 1196 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 55.81 119.23 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " pdb=" CG ASP A 256 " pdb=" OD1 ASP A 256 " ideal model delta sinusoidal sigma weight residual -30.00 -86.92 56.92 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA GLU A 366 " pdb=" CB GLU A 366 " pdb=" CG GLU A 366 " pdb=" CD GLU A 366 " ideal model delta sinusoidal sigma weight residual -180.00 -121.79 -58.21 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 441 0.079 - 0.158: 53 0.158 - 0.237: 3 0.237 - 0.316: 3 0.316 - 0.395: 3 Chirality restraints: 503 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.35 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 500 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.104 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C5N NDP A 500 " 0.256 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.262 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.059 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C3N NDP A 500 " 0.166 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " -0.038 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.106 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 144 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.050 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 859 2.80 - 3.33: 3195 3.33 - 3.85: 5729 3.85 - 4.38: 6963 4.38 - 4.90: 11740 Nonbonded interactions: 28486 Sorted by model distance: nonbonded pdb=" OE2 GLU A 114 " pdb=" O HOH A 601 " model vdw 2.278 3.040 nonbonded pdb=" NE ARG A 73 " pdb=" OE2 GLU A 78 " model vdw 2.476 3.120 nonbonded pdb=" O VAL A 348 " pdb=" OG SER A 351 " model vdw 2.493 3.040 nonbonded pdb=" OD2 ASP A 47 " pdb=" OG SER A 116 " model vdw 2.517 3.040 nonbonded pdb=" OE1 GLN A 357 " pdb=" O HOH A 602 " model vdw 2.518 3.040 ... (remaining 28481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.570 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- 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= 0.357 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 122 TYR 0.008 0.001 TYR A 363 PHE 0.010 0.001 PHE A 341 TRP 0.009 0.001 TRP A 30 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00895 ( 3410) covalent geometry : angle 1.08968 ( 4635) hydrogen bonds : bond 0.13181 ( 183) hydrogen bonds : angle 6.34081 ( 575) *********************** 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 : 0.105 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: 0.6702 time to fit residues: 54.8309 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 : 0.080 ------------------------------------------------------------------------------- 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 24 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3210 r_free = 0.3210 target = 0.112079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.087811 restraints weight = 11667.255| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.80 r_work: 0.2550 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3410 Z= 0.179 Angle : 0.540 4.710 4635 Z= 0.284 Chirality : 0.045 0.177 503 Planarity : 0.006 0.073 589 Dihedral : 8.500 125.230 477 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 9.41 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.43), residues: 416 helix: 2.24 (0.35), residues: 212 sheet: -0.51 (0.68), residues: 68 loop : -0.02 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.011 0.001 TYR A 363 PHE 0.013 0.002 PHE A 341 TRP 0.008 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3410) covalent geometry : angle 0.53966 ( 4635) hydrogen bonds : bond 0.04427 ( 183) hydrogen bonds : angle 4.60558 ( 575) *********************** 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 77 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.128 Fit side-chains REVERT: A 277 THR cc_start: 0.8149 (m) cc_final: 0.7719 (p) REVERT: A 283 GLU cc_start: 0.7615 (tt0) cc_final: 0.7337 (mt-10) REVERT: A 287 LEU cc_start: 0.8664 (mt) cc_final: 0.8433 (mp) REVERT: A 303 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: A 419 LYS cc_start: 0.8014 (mttt) cc_final: 0.7792 (mttt) outliers start: 9 outliers final: 3 residues processed: 72 average time/residue: 0.6294 time to fit residues: 46.4010 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 : 0.129 ------------------------------------------------------------------------------- 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 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3179 r_free = 0.3179 target = 0.109980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.087076 restraints weight = 6775.743| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.12 r_work: 0.2586 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3410 Z= 0.172 Angle : 0.521 4.969 4635 Z= 0.273 Chirality : 0.045 0.165 503 Planarity : 0.005 0.064 589 Dihedral : 7.683 113.908 468 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 2.35 % Allowed : 13.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.43), residues: 416 helix: 2.22 (0.34), residues: 210 sheet: -0.20 (0.66), residues: 72 loop : -0.23 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.010 0.001 TYR A 363 PHE 0.012 0.002 PHE A 341 TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3410) covalent geometry : angle 0.52060 ( 4635) hydrogen bonds : bond 0.04346 ( 183) hydrogen bonds : angle 4.38716 ( 575) *********************** 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 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.134 Fit side-chains REVERT: A 283 GLU cc_start: 0.7666 (tt0) cc_final: 0.7425 (mt-10) REVERT: A 303 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8393 (pt0) REVERT: A 419 LYS cc_start: 0.7981 (mttt) cc_final: 0.7747 (mttt) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.6857 time to fit residues: 42.8860 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.113410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.091619 restraints weight = 4458.105| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.68 r_work: 0.2745 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.52 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 = 0.40 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: 0.8810 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3410 Z= 0.119 Angle : 0.505 9.704 4635 Z= 0.261 Chirality : 0.043 0.138 503 Planarity : 0.005 0.055 589 Dihedral : 7.147 98.340 468 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.41 % Favored : 97.35 % Rotamer: Outliers : 2.35 % Allowed : 13.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.43), residues: 416 helix: 2.28 (0.34), residues: 211 sheet: -0.12 (0.66), residues: 72 loop : -0.16 (0.58), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.008 0.001 TYR A 363 PHE 0.008 0.001 PHE A 341 TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3410) covalent geometry : angle 0.50533 ( 4635) hydrogen bonds : bond 0.03654 ( 183) hydrogen bonds : angle 4.15540 ( 575) *********************** 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 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.128 Fit side-chains REVERT: A 303 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: A 366 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7730 (mt-10) outliers start: 8 outliers final: 1 residues processed: 66 average time/residue: 0.6407 time to fit residues: 43.4002 Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.112529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.089676 restraints weight = 6689.644| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.06 r_work: 0.2604 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3410 Z= 0.166 Angle : 0.544 12.884 4635 Z= 0.277 Chirality : 0.044 0.152 503 Planarity : 0.005 0.050 589 Dihedral : 6.934 80.198 468 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 2.35 % Allowed : 14.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.42), residues: 416 helix: 2.19 (0.35), residues: 210 sheet: -0.18 (0.66), residues: 72 loop : -0.21 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.011 0.001 TYR A 363 PHE 0.013 0.002 PHE A 341 TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3410) covalent geometry : angle 0.54442 ( 4635) hydrogen bonds : bond 0.04174 ( 183) hydrogen bonds : angle 4.26756 ( 575) *********************** 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 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.136 Fit side-chains REVERT: A 286 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: A 303 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8415 (pt0) outliers start: 8 outliers final: 2 residues processed: 63 average time/residue: 0.6405 time to fit residues: 41.3241 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 : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.115254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.091787 restraints weight = 8330.577| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.34 r_work: 0.2707 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3410 Z= 0.108 Angle : 0.504 12.195 4635 Z= 0.256 Chirality : 0.043 0.127 503 Planarity : 0.005 0.047 589 Dihedral : 6.284 69.257 468 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 14.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.43), residues: 416 helix: 2.30 (0.34), residues: 211 sheet: -0.03 (0.66), residues: 72 loop : -0.15 (0.58), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.007 0.001 TYR A 363 PHE 0.009 0.001 PHE A 341 TRP 0.007 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3410) covalent geometry : angle 0.50392 ( 4635) hydrogen bonds : bond 0.03408 ( 183) hydrogen bonds : angle 4.05558 ( 575) *********************** 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 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.095 Fit side-chains REVERT: A 41 SER cc_start: 0.9052 (m) cc_final: 0.8683 (p) REVERT: A 303 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: A 366 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7764 (mt-10) outliers start: 7 outliers final: 1 residues processed: 64 average time/residue: 0.6154 time to fit residues: 40.3692 Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 overall best weight: 1.7704 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.112794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.089366 restraints weight = 8092.845| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.31 r_work: 0.2717 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3410 Z= 0.142 Angle : 0.515 11.405 4635 Z= 0.263 Chirality : 0.044 0.139 503 Planarity : 0.005 0.046 589 Dihedral : 5.838 57.691 468 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 2.35 % Allowed : 13.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.43), residues: 416 helix: 2.28 (0.35), residues: 210 sheet: -0.10 (0.66), residues: 72 loop : -0.17 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.009 0.001 TYR A 363 PHE 0.012 0.001 PHE A 341 TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3410) covalent geometry : angle 0.51539 ( 4635) hydrogen bonds : bond 0.03915 ( 183) hydrogen bonds : angle 4.16957 ( 575) *********************** 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 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.109 Fit side-chains REVERT: A 41 SER cc_start: 0.9060 (m) cc_final: 0.8707 (p) REVERT: A 303 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: A 366 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7759 (mt-10) outliers start: 8 outliers final: 1 residues processed: 62 average time/residue: 0.6362 time to fit residues: 40.4551 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 : 0.134 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.113484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.089491 restraints weight = 11412.707| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.72 r_work: 0.2669 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3410 Z= 0.147 Angle : 0.520 7.986 4635 Z= 0.271 Chirality : 0.044 0.140 503 Planarity : 0.005 0.045 589 Dihedral : 5.352 47.029 468 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 1.47 % Allowed : 14.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.42), residues: 416 helix: 2.39 (0.35), residues: 205 sheet: -0.05 (0.74), residues: 58 loop : -0.39 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.009 0.001 TYR A 363 PHE 0.012 0.002 PHE A 341 TRP 0.007 0.001 TRP A 263 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3410) covalent geometry : angle 0.52008 ( 4635) hydrogen bonds : bond 0.03919 ( 183) hydrogen bonds : angle 4.17984 ( 575) *********************** 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.135 Fit side-chains REVERT: A 41 SER cc_start: 0.9022 (m) cc_final: 0.8683 (p) REVERT: A 303 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8448 (pt0) outliers start: 5 outliers final: 1 residues processed: 60 average time/residue: 0.6754 time to fit residues: 41.5309 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 379 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 34 optimal weight: 0.0050 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 overall best weight: 1.9876 ------------------------------------------------------------------------------- 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 = 0.3196 r_free = 0.3196 target = 0.111197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.086942 restraints weight = 11659.377| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.78 r_work: 0.2578 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.004 0.051 3410 Z= 0.157 Angle : 0.517 8.090 4635 Z= 0.272 Chirality : 0.044 0.143 503 Planarity : 0.005 0.046 589 Dihedral : 4.935 43.550 465 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.76 % Allowed : 14.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.42), residues: 416 helix: 2.36 (0.35), residues: 205 sheet: -0.14 (0.74), residues: 58 loop : -0.38 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.010 0.001 TYR A 363 PHE 0.012 0.002 PHE A 341 TRP 0.008 0.001 TRP A 263 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3410) covalent geometry : angle 0.51719 ( 4635) hydrogen bonds : bond 0.04052 ( 183) hydrogen bonds : angle 4.23083 ( 575) *********************** 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.138 Fit side-chains REVERT: A 41 SER cc_start: 0.9002 (m) cc_final: 0.8622 (p) REVERT: A 246 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.7120 (mpt180) REVERT: A 303 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8434 (pt0) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.6537 time to fit residues: 40.2785 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 303 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 0 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.111893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.089196 restraints weight = 6370.161| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.02 r_work: 0.2721 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3410 Z= 0.143 Angle : 0.517 7.955 4635 Z= 0.271 Chirality : 0.043 0.138 503 Planarity : 0.005 0.046 589 Dihedral : 4.849 41.635 465 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.42), residues: 416 helix: 2.38 (0.35), residues: 205 sheet: -0.07 (0.74), residues: 58 loop : -0.40 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.009 0.001 TYR A 363 PHE 0.012 0.001 PHE A 341 TRP 0.009 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3410) covalent geometry : angle 0.51724 ( 4635) hydrogen bonds : bond 0.03879 ( 183) hydrogen bonds : angle 4.18900 ( 575) ********************** 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.136 Fit side-chains REVERT: A 41 SER cc_start: 0.9048 (m) cc_final: 0.8701 (p) REVERT: A 246 ARG cc_start: 0.7717 (mmt-90) cc_final: 0.7245 (mpt180) REVERT: A 303 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8474 (pt0) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.6700 time to fit residues: 41.9381 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 303 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 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.0070 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.116216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.092110 restraints weight = 11405.525| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.77 r_work: 0.2708 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3410 Z= 0.107 Angle : 0.506 8.251 4635 Z= 0.261 Chirality : 0.042 0.124 503 Planarity : 0.005 0.046 589 Dihedral : 4.657 40.109 465 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 0.88 % Allowed : 16.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.43), residues: 416 helix: 2.28 (0.35), residues: 211 sheet: -0.10 (0.65), residues: 73 loop : -0.09 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.006 0.001 TYR A 363 PHE 0.008 0.001 PHE A 341 TRP 0.009 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3410) covalent geometry : angle 0.50609 ( 4635) hydrogen bonds : bond 0.03304 ( 183) hydrogen bonds : angle 4.07614 ( 575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1534.55 seconds wall clock time: 26 minutes 55.09 seconds (1615.09 seconds total)