Starting phenix.real_space_refine on Wed Sep 17 03:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xco_38249/09_2025/8xco_38249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xco_38249/09_2025/8xco_38249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xco_38249/09_2025/8xco_38249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xco_38249/09_2025/8xco_38249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xco_38249/09_2025/8xco_38249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xco_38249/09_2025/8xco_38249.map" } resolution = 2.64 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 2115 2.51 5 N 565 2.21 5 O 638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3335 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} 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: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} 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: 3321 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 62 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 14} Link IDs: {None: 14} Time building chain proxies: 1.65, per 1000 atoms: 0.49 Number of scatterers: 3335 At special positions: 0 Unit cell: (69.936, 68.432, 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 638 8.00 N 565 7.00 C 2115 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: 0.28 Conformation dependent library (CDL) restraints added in 240.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 17 helices and 3 sheets defined 54.6% alpha, 19.0% 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: 3.525A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.958A 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 164 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 removed outlier: 3.520A pdb=" N THR A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) 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: 6.421A 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: 7.735A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.911A 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: 6.405A 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: 8.284A 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: 6.416A 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) 197 hydrogen bonds defined for protein. 569 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: 0.53 Time building geometry restraints manager: 0.38 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: 1068 1.34 - 1.46: 583 1.46 - 1.57: 1720 1.57 - 1.69: 3 1.69 - 1.80: 27 Bond restraints: 3401 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.616 -0.092 1.29e-02 6.01e+03 5.12e+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 5.06e+01 bond pdb=" C GLY A 183 " pdb=" N SER A 184 " ideal model delta sigma weight residual 1.331 1.436 -0.105 1.51e-02 4.39e+03 4.85e+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 3.22e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 4580 4.41 - 8.82: 25 8.82 - 13.24: 13 13.24 - 17.65: 4 17.65 - 22.06: 1 Bond angle restraints: 4623 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 105.41 127.47 -22.06 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 103.84 119.18 -15.34 1.91e+00 2.73e-01 6.42e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.34 -14.60 1.95e+00 2.62e-01 5.58e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.47 7.99 1.17e+00 7.36e-01 4.69e+01 angle pdb=" O2X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.33 108.95 8.38 1.48e+00 4.57e-01 3.21e+01 ... (remaining 4618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.83: 1835 23.83 - 47.67: 137 47.67 - 71.50: 36 71.50 - 95.34: 4 95.34 - 119.17: 1 Dihedral angle restraints: 2013 sinusoidal: 820 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 55.87 119.17 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 -86.85 56.85 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " pdb=" OD1 ASN A 319 " ideal model delta sinusoidal sigma weight residual -90.00 -159.73 69.73 2 2.00e+01 2.50e-03 1.06e+01 ... (remaining 2010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 433 0.079 - 0.158: 59 0.158 - 0.236: 4 0.236 - 0.315: 3 0.315 - 0.394: 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 3.88e+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 -2.34 -0.36 2.00e-01 2.50e+01 3.32e+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 3.12e+00 ... (remaining 499 not shown) Planarity restraints: 587 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 3.92e+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 1.26e+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 584 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1329 2.92 - 3.41: 3324 3.41 - 3.91: 5836 3.91 - 4.40: 6734 4.40 - 4.90: 11087 Nonbonded interactions: 28310 Sorted by model distance: nonbonded pdb=" OH TYR A 352 " pdb=" O HOH A 601 " model vdw 2.424 3.040 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 602 " model vdw 2.446 3.120 nonbonded pdb=" O ILE A 174 " pdb=" NZ LYS A 177 " model vdw 2.505 3.120 nonbonded pdb=" OD2 ASP A 47 " pdb=" OG SER A 116 " model vdw 2.516 3.040 nonbonded pdb=" O2B NDP A 500 " pdb=" O3B NDP A 500 " model vdw 2.532 2.432 ... (remaining 28305 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.700 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 3401 Z= 0.387 Angle : 1.129 22.060 4623 Z= 0.602 Chirality : 0.060 0.394 502 Planarity : 0.011 0.198 587 Dihedral : 17.486 119.173 1253 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.78 % Allowed : 4.72 % Favored : 88.50 % 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: 0.92 (0.42), residues: 415 helix: 1.60 (0.35), residues: 211 sheet: -0.20 (0.69), residues: 66 loop : -0.44 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 200 TYR 0.004 0.001 TYR A 101 PHE 0.010 0.001 PHE A 341 TRP 0.009 0.001 TRP A 30 HIS 0.001 0.000 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00918 ( 3401) covalent geometry : angle 1.12863 ( 4623) hydrogen bonds : bond 0.14316 ( 181) hydrogen bonds : angle 6.60510 ( 569) *********************** 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 119 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.164 Fit side-chains REVERT: A 149 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8638 (p0) REVERT: A 263 TRP cc_start: 0.8650 (t-100) cc_final: 0.8322 (t-100) REVERT: A 310 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8028 (mttp) outliers start: 23 outliers final: 1 residues processed: 105 average time/residue: 0.6373 time to fit residues: 68.5335 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 310 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 337 GLN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.076374 restraints weight = 11111.404| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.55 r_work: 0.2625 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.121 Angle : 0.499 6.600 4623 Z= 0.257 Chirality : 0.042 0.150 502 Planarity : 0.005 0.071 587 Dihedral : 7.703 121.351 471 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.65 % Allowed : 17.40 % Favored : 79.94 % 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: 1.76 (0.44), residues: 415 helix: 2.26 (0.36), residues: 213 sheet: 0.33 (0.76), residues: 58 loop : -0.09 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 16 TYR 0.008 0.001 TYR A 363 PHE 0.008 0.001 PHE A 381 TRP 0.012 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3401) covalent geometry : angle 0.49884 ( 4623) hydrogen bonds : bond 0.03846 ( 181) hydrogen bonds : angle 4.38013 ( 569) *********************** 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 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.144 Fit side-chains REVERT: A 262 LYS cc_start: 0.8649 (tttp) cc_final: 0.8375 (tttm) REVERT: A 263 TRP cc_start: 0.8813 (t-100) cc_final: 0.8521 (t-100) REVERT: A 266 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8456 (mt-10) outliers start: 9 outliers final: 3 residues processed: 64 average time/residue: 0.6803 time to fit residues: 44.6606 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.0670 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.074806 restraints weight = 4434.682| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 1.57 r_work: 0.2628 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3401 Z= 0.138 Angle : 0.485 5.231 4623 Z= 0.256 Chirality : 0.043 0.149 502 Planarity : 0.005 0.059 587 Dihedral : 6.547 94.842 466 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.36 % Allowed : 17.70 % Favored : 79.94 % 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: 1.76 (0.43), residues: 415 helix: 2.25 (0.35), residues: 213 sheet: 0.21 (0.69), residues: 70 loop : -0.02 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.012 0.001 TYR A 363 PHE 0.009 0.001 PHE A 381 TRP 0.015 0.002 TRP A 364 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3401) covalent geometry : angle 0.48516 ( 4623) hydrogen bonds : bond 0.04107 ( 181) hydrogen bonds : angle 4.20131 ( 569) *********************** 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 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.202 Fit side-chains REVERT: A 263 TRP cc_start: 0.8787 (t-100) cc_final: 0.8523 (t-100) REVERT: A 312 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8528 (mtpt) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 0.5944 time to fit residues: 35.5257 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 : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.074125 restraints weight = 11358.962| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.53 r_work: 0.2581 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.115 Angle : 0.463 5.306 4623 Z= 0.241 Chirality : 0.042 0.136 502 Planarity : 0.005 0.054 587 Dihedral : 6.122 81.323 466 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.36 % Allowed : 17.70 % Favored : 79.94 % 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: 1.80 (0.43), residues: 415 helix: 2.37 (0.35), residues: 213 sheet: 0.05 (0.68), residues: 72 loop : -0.06 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.009 0.001 TYR A 363 PHE 0.008 0.001 PHE A 381 TRP 0.010 0.001 TRP A 364 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3401) covalent geometry : angle 0.46310 ( 4623) hydrogen bonds : bond 0.03575 ( 181) hydrogen bonds : angle 3.98454 ( 569) *********************** 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 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.138 Fit side-chains REVERT: A 78 GLU cc_start: 0.8456 (tp30) cc_final: 0.8202 (mm-30) REVERT: A 263 TRP cc_start: 0.8806 (t-100) cc_final: 0.8554 (t-100) REVERT: A 266 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8580 (mt-10) REVERT: A 392 ASN cc_start: 0.8927 (t0) cc_final: 0.8400 (t0) outliers start: 8 outliers final: 3 residues processed: 62 average time/residue: 0.5660 time to fit residues: 36.1262 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN 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 = 0.103881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.071460 restraints weight = 6528.666| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 1.91 r_work: 0.2498 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2382 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3401 Z= 0.218 Angle : 0.532 5.467 4623 Z= 0.281 Chirality : 0.046 0.161 502 Planarity : 0.005 0.053 587 Dihedral : 6.148 76.829 466 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.06 % Allowed : 17.40 % 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 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: 1.58 (0.43), residues: 415 helix: 2.13 (0.34), residues: 211 sheet: 0.03 (0.68), residues: 72 loop : -0.05 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.016 0.002 TYR A 363 PHE 0.012 0.002 PHE A 381 TRP 0.019 0.002 TRP A 364 HIS 0.002 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 3401) covalent geometry : angle 0.53232 ( 4623) hydrogen bonds : bond 0.04678 ( 181) hydrogen bonds : angle 4.35853 ( 569) *********************** 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 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.137 Fit side-chains REVERT: A 9 MET cc_start: 0.8579 (mmm) cc_final: 0.8371 (tpp) REVERT: A 149 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8864 (p0) REVERT: A 263 TRP cc_start: 0.8765 (t-100) cc_final: 0.8555 (t-100) REVERT: A 392 ASN cc_start: 0.8942 (t0) cc_final: 0.8436 (t0) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.6070 time to fit residues: 34.3420 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 : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.071853 restraints weight = 11052.701| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 2.47 r_work: 0.2486 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3401 Z= 0.154 Angle : 0.493 5.556 4623 Z= 0.260 Chirality : 0.044 0.141 502 Planarity : 0.005 0.049 587 Dihedral : 5.870 71.860 466 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 17.70 % 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 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: 1.57 (0.43), residues: 415 helix: 2.17 (0.34), residues: 213 sheet: 0.00 (0.67), residues: 72 loop : -0.18 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.012 0.001 TYR A 363 PHE 0.011 0.002 PHE A 381 TRP 0.013 0.001 TRP A 364 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3401) covalent geometry : angle 0.49279 ( 4623) hydrogen bonds : bond 0.04109 ( 181) hydrogen bonds : angle 4.18170 ( 569) *********************** 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 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.143 Fit side-chains REVERT: A 149 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8835 (p0) REVERT: A 263 TRP cc_start: 0.8755 (t-100) cc_final: 0.8536 (t-100) REVERT: A 392 ASN cc_start: 0.8948 (t0) cc_final: 0.8420 (t0) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.5663 time to fit residues: 29.7773 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.075122 restraints weight = 11350.462| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.45 r_work: 0.2603 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3401 Z= 0.099 Angle : 0.455 5.671 4623 Z= 0.236 Chirality : 0.042 0.127 502 Planarity : 0.005 0.048 587 Dihedral : 5.261 59.231 466 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.88 % Allowed : 18.58 % 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 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: 1.70 (0.43), residues: 415 helix: 2.42 (0.35), residues: 213 sheet: 0.16 (0.72), residues: 62 loop : -0.43 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.007 0.001 TYR A 250 PHE 0.009 0.001 PHE A 381 TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3401) covalent geometry : angle 0.45477 ( 4623) hydrogen bonds : bond 0.03358 ( 181) hydrogen bonds : angle 3.88590 ( 569) *********************** 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 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.143 Fit side-chains REVERT: A 149 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8590 (p0) REVERT: A 263 TRP cc_start: 0.8770 (t-100) cc_final: 0.8543 (t-100) outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 0.6302 time to fit residues: 34.3396 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.076432 restraints weight = 6589.103| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.93 r_work: 0.2636 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3401 Z= 0.103 Angle : 0.461 6.373 4623 Z= 0.239 Chirality : 0.042 0.126 502 Planarity : 0.005 0.048 587 Dihedral : 4.869 45.767 466 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.88 % Allowed : 17.99 % 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 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: 1.89 (0.43), residues: 415 helix: 2.53 (0.35), residues: 212 sheet: 0.08 (0.67), residues: 72 loop : -0.15 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.007 0.001 TYR A 363 PHE 0.008 0.001 PHE A 381 TRP 0.007 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3401) covalent geometry : angle 0.46092 ( 4623) hydrogen bonds : bond 0.03398 ( 181) hydrogen bonds : angle 3.87296 ( 569) *********************** 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 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.138 Fit side-chains REVERT: A 78 GLU cc_start: 0.8354 (tp30) cc_final: 0.8104 (mm-30) REVERT: A 263 TRP cc_start: 0.8756 (t-100) cc_final: 0.8533 (t-100) REVERT: A 392 ASN cc_start: 0.8932 (t0) cc_final: 0.8394 (t0) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.6089 time to fit residues: 31.9874 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 0.0060 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.079675 restraints weight = 6593.484| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.90 r_work: 0.2701 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3401 Z= 0.090 Angle : 0.456 7.226 4623 Z= 0.232 Chirality : 0.041 0.126 502 Planarity : 0.004 0.049 587 Dihedral : 4.432 41.977 464 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 19.47 % 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 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: 2.00 (0.43), residues: 415 helix: 2.65 (0.35), residues: 212 sheet: 0.16 (0.68), residues: 70 loop : -0.17 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.006 0.001 TYR A 160 PHE 0.006 0.001 PHE A 381 TRP 0.008 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 3401) covalent geometry : angle 0.45606 ( 4623) hydrogen bonds : bond 0.02984 ( 181) hydrogen bonds : angle 3.70392 ( 569) *********************** 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 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.180 Fit side-chains REVERT: A 78 GLU cc_start: 0.8322 (tp30) cc_final: 0.8095 (mm-30) REVERT: A 263 TRP cc_start: 0.8737 (t-100) cc_final: 0.8532 (t-100) REVERT: A 392 ASN cc_start: 0.8893 (t0) cc_final: 0.8354 (t0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.6214 time to fit residues: 33.2399 Evaluate side-chains 49 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 chunk 21 optimal weight: 0.0060 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.077750 restraints weight = 11154.161| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.48 r_work: 0.2653 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3401 Z= 0.093 Angle : 0.462 7.317 4623 Z= 0.237 Chirality : 0.041 0.126 502 Planarity : 0.004 0.047 587 Dihedral : 4.401 42.179 464 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.29 % Allowed : 19.76 % Favored : 79.94 % 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: 2.01 (0.43), residues: 415 helix: 2.62 (0.35), residues: 212 sheet: 0.20 (0.69), residues: 70 loop : -0.13 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 406 TYR 0.006 0.001 TYR A 408 PHE 0.007 0.001 PHE A 381 TRP 0.008 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 3401) covalent geometry : angle 0.46157 ( 4623) hydrogen bonds : bond 0.03101 ( 181) hydrogen bonds : angle 3.70619 ( 569) ********************** 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 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.156 Fit side-chains REVERT: A 78 GLU cc_start: 0.8422 (tp30) cc_final: 0.8197 (mm-30) REVERT: A 263 TRP cc_start: 0.8750 (t-100) cc_final: 0.8545 (t-100) REVERT: A 392 ASN cc_start: 0.8918 (t0) cc_final: 0.8368 (t0) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.5652 time to fit residues: 29.6677 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 : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.076425 restraints weight = 7751.767| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.03 r_work: 0.2636 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.109 Angle : 0.473 7.143 4623 Z= 0.243 Chirality : 0.042 0.127 502 Planarity : 0.004 0.048 587 Dihedral : 4.410 41.846 464 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.29 % Allowed : 20.06 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.98 (0.43), residues: 415 helix: 2.61 (0.35), residues: 212 sheet: 0.15 (0.69), residues: 70 loop : -0.14 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 406 TYR 0.009 0.001 TYR A 363 PHE 0.008 0.001 PHE A 381 TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3401) covalent geometry : angle 0.47350 ( 4623) hydrogen bonds : bond 0.03397 ( 181) hydrogen bonds : angle 3.79479 ( 569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.54 seconds wall clock time: 29 minutes 50.90 seconds (1790.90 seconds total)