Starting phenix.real_space_refine on Thu Jul 2 00:16:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmo_66099/07_2026/9wmo_66099_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmo_66099/07_2026/9wmo_66099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wmo_66099/07_2026/9wmo_66099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmo_66099/07_2026/9wmo_66099.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmo_66099/07_2026/9wmo_66099_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmo_66099/07_2026/9wmo_66099_neut.cif" } resolution = 3.01 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= -0.004 sd= 0.110 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2992 2.51 5 N 657 2.21 5 O 720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4405 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4263 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 26, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 2 Time building chain proxies: 0.82, per 1000 atoms: 0.19 Number of scatterers: 4405 At special positions: 0 Unit cell: (82.159, 69.355, 82.159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 1 11.00 O 720 8.00 N 657 7.00 C 2992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " distance=2.03 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: 0.22 Conformation dependent library (CDL) restraints added in 114.1 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 78.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.537A pdb=" N LEU A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.548A pdb=" N LEU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.601A pdb=" N TRP A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.994A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.190A pdb=" N HIS A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.517A pdb=" N THR A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.042A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 300 removed outlier: 4.243A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.823A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 365 through 376 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.563A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.791A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.643A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.839A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 290 hydrogen bonds defined for protein. 846 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: 0.44 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 626 1.31 - 1.44: 1318 1.44 - 1.56: 2553 1.56 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4551 Sorted by residual: bond pdb=" C SER A 381 " pdb=" O SER A 381 " ideal model delta sigma weight residual 1.238 1.186 0.051 1.28e-02 6.10e+03 1.62e+01 bond pdb=" N SER A 381 " pdb=" CA SER A 381 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.41e-02 5.03e+03 1.21e+01 bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.500 -0.040 1.19e-02 7.06e+03 1.11e+01 bond pdb=" C ILE A 479 " pdb=" O ILE A 479 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.32e-02 5.74e+03 1.08e+01 bond pdb=" N GLN A 522 " pdb=" CA GLN A 522 " ideal model delta sigma weight residual 1.462 1.496 -0.033 1.05e-02 9.07e+03 1.01e+01 ... (remaining 4546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 5769 1.52 - 3.04: 354 3.04 - 4.56: 89 4.56 - 6.08: 19 6.08 - 7.60: 2 Bond angle restraints: 6233 Sorted by residual: angle pdb=" N ARG A 321 " pdb=" CA ARG A 321 " pdb=" C ARG A 321 " ideal model delta sigma weight residual 111.11 105.37 5.74 1.20e+00 6.94e-01 2.29e+01 angle pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" O LEU A 395 " ideal model delta sigma weight residual 120.82 116.33 4.49 1.05e+00 9.07e-01 1.83e+01 angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.64 4.18 1.05e+00 9.07e-01 1.58e+01 angle pdb=" CA LEU A 503 " pdb=" C LEU A 503 " pdb=" O LEU A 503 " ideal model delta sigma weight residual 120.42 116.31 4.11 1.06e+00 8.90e-01 1.50e+01 angle pdb=" N MET A 135 " pdb=" CA MET A 135 " pdb=" C MET A 135 " ideal model delta sigma weight residual 111.71 107.30 4.41 1.15e+00 7.56e-01 1.47e+01 ... (remaining 6228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 2583 23.98 - 47.95: 196 47.95 - 71.92: 31 71.92 - 95.90: 1 95.90 - 119.87: 10 Dihedral angle restraints: 2821 sinusoidal: 1271 harmonic: 1550 Sorted by residual: dihedral pdb=" C1 CLR A 706 " pdb=" C2 CLR A 706 " pdb=" C3 CLR A 706 " pdb=" O1 CLR A 706 " ideal model delta sinusoidal sigma weight residual 180.04 60.17 119.87 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C10 CLR A 705 " pdb=" C1 CLR A 705 " pdb=" C2 CLR A 705 " pdb=" C3 CLR A 705 " ideal model delta sinusoidal sigma weight residual -56.83 62.25 -119.08 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C1 CLR A 706 " pdb=" C2 CLR A 706 " pdb=" C3 CLR A 706 " pdb=" C4 CLR A 706 " ideal model delta sinusoidal sigma weight residual 57.41 -61.45 118.86 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 2818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 532 0.044 - 0.089: 111 0.089 - 0.133: 56 0.133 - 0.177: 12 0.177 - 0.221: 3 Chirality restraints: 714 Sorted by residual: chirality pdb=" CA ASN A 134 " pdb=" N ASN A 134 " pdb=" C ASN A 134 " pdb=" CB ASN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA GLN A 400 " pdb=" N GLN A 400 " pdb=" C GLN A 400 " pdb=" CB GLN A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA MET A 122 " pdb=" N MET A 122 " pdb=" C MET A 122 " pdb=" CB MET A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 711 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 321 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ARG A 321 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG A 321 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP A 322 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 402 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ALA A 402 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 402 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 403 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " 0.044 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO A 523 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " 0.036 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1549 2.86 - 3.37: 4434 3.37 - 3.88: 7837 3.88 - 4.39: 9502 4.39 - 4.90: 15379 Nonbonded interactions: 38701 Sorted by model distance: nonbonded pdb=" O LEU A 144 " pdb=" OG SER A 147 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 2.354 3.210 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 536 " model vdw 2.383 3.040 nonbonded pdb=" OD1 ASN A 59 " pdb="NA NA A 701 " model vdw 2.424 3.210 nonbonded pdb=" O PHE A 339 " pdb=" OG SER A 343 " model vdw 2.433 3.040 ... (remaining 38696 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=1.00 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: 1.380 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.940 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.005 0.058 4552 Z= 0.354 Angle : 0.846 7.597 6235 Z= 0.554 Chirality : 0.048 0.221 714 Planarity : 0.007 0.066 726 Dihedral : 17.911 119.873 1836 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 18.98 % Favored : 81.02 % 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 are not related in a simple way. whole: 0.24 (0.35), residues: 536 helix: 0.86 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.43 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 420 TYR 0.016 0.002 TYR A 132 PHE 0.012 0.001 PHE A 245 TRP 0.027 0.002 TRP A 215 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.35 ( 4551) covalent geometry : angle 0.84632 / 0.55 ( 6233) SS BOND : bond 0.00293 / 0.15 ( 1) SS BOND : angle 0.51859 / 0.30 ( 2) hydrogen bonds : bond 0.12732 / 8.32 ( 290) hydrogen bonds : angle 6.03806 / 4.13 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 234 LYS cc_start: 0.7863 (tppt) cc_final: 0.6807 (tmtt) REVERT: A 286 LYS cc_start: 0.8501 (tttt) cc_final: 0.8258 (ttpp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0542 time to fit residues: 8.8685 Evaluate side-chains 89 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.150237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131767 restraints weight = 5272.793| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.81 r_work: 0.3479 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4552 Z= 0.175 Angle : 0.611 7.107 6235 Z= 0.298 Chirality : 0.040 0.153 714 Planarity : 0.005 0.047 726 Dihedral : 8.428 59.319 909 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.97 % Allowed : 15.67 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.35), residues: 536 helix: 1.82 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.10 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 568 TYR 0.019 0.002 TYR A 132 PHE 0.015 0.002 PHE A 91 TRP 0.014 0.002 TRP A 215 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 4551) covalent geometry : angle 0.61087 / 0.30 ( 6233) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 0.19594 / 0.11 ( 2) hydrogen bonds : bond 0.04824 / 3.15 ( 290) hydrogen bonds : angle 4.80630 / 3.31 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.085 Fit side-chains REVERT: A 133 TYR cc_start: 0.8045 (m-10) cc_final: 0.7624 (m-10) REVERT: A 239 SER cc_start: 0.5921 (OUTLIER) cc_final: 0.5702 (t) REVERT: A 351 GLU cc_start: 0.8351 (tp30) cc_final: 0.8009 (tp30) REVERT: A 385 SER cc_start: 0.9196 (t) cc_final: 0.8900 (t) REVERT: A 413 ASP cc_start: 0.8197 (m-30) cc_final: 0.7695 (m-30) REVERT: A 418 TYR cc_start: 0.8137 (t80) cc_final: 0.7936 (t80) REVERT: A 525 GLU cc_start: 0.8265 (pt0) cc_final: 0.7954 (mt-10) REVERT: A 545 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7074 (tp) REVERT: A 569 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8108 (mm) outliers start: 18 outliers final: 9 residues processed: 98 average time/residue: 0.0371 time to fit residues: 5.1176 Evaluate side-chains 94 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126746 restraints weight = 5207.004| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.81 r_work: 0.3342 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4552 Z= 0.151 Angle : 0.530 5.465 6235 Z= 0.266 Chirality : 0.039 0.139 714 Planarity : 0.004 0.042 726 Dihedral : 7.587 57.381 909 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.97 % Allowed : 13.69 % Favored : 82.34 % 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 are not related in a simple way. whole: 1.82 (0.36), residues: 536 helix: 2.07 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.91 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.016 0.001 TYR A 132 PHE 0.015 0.001 PHE A 460 TRP 0.009 0.001 TRP A 109 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4551) covalent geometry : angle 0.53013 / 0.27 ( 6233) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 1.13599 / 0.62 ( 2) hydrogen bonds : bond 0.04664 / 3.03 ( 290) hydrogen bonds : angle 4.66572 / 3.22 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8016 (m-10) cc_final: 0.7592 (m-10) REVERT: A 385 SER cc_start: 0.9246 (t) cc_final: 0.8945 (t) REVERT: A 413 ASP cc_start: 0.8212 (m-30) cc_final: 0.7643 (m-30) REVERT: A 545 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6960 (tp) REVERT: A 569 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (mm) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.0366 time to fit residues: 4.8143 Evaluate side-chains 90 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114918 restraints weight = 5350.176| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.66 r_work: 0.3198 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4552 Z= 0.167 Angle : 0.537 5.508 6235 Z= 0.268 Chirality : 0.040 0.141 714 Planarity : 0.004 0.036 726 Dihedral : 7.768 59.547 909 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.53 % Allowed : 14.79 % Favored : 81.68 % 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 are not related in a simple way. whole: 1.82 (0.36), residues: 536 helix: 2.06 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.86 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.015 0.001 TYR A 132 PHE 0.018 0.001 PHE A 91 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 4551) covalent geometry : angle 0.53720 / 0.27 ( 6233) SS BOND : bond 0.00273 / 0.14 ( 1) SS BOND : angle 0.73885 / 0.41 ( 2) hydrogen bonds : bond 0.04725 / 3.05 ( 290) hydrogen bonds : angle 4.68492 / 3.23 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8046 (m-10) cc_final: 0.7689 (m-10) REVERT: A 259 VAL cc_start: 0.8911 (t) cc_final: 0.8694 (t) REVERT: A 385 SER cc_start: 0.9311 (t) cc_final: 0.8992 (t) REVERT: A 413 ASP cc_start: 0.8186 (m-30) cc_final: 0.7540 (m-30) REVERT: A 525 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: A 569 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8166 (mm) outliers start: 16 outliers final: 9 residues processed: 90 average time/residue: 0.0413 time to fit residues: 5.2700 Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130087 restraints weight = 5325.206| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.78 r_work: 0.3415 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4552 Z= 0.138 Angle : 0.509 5.340 6235 Z= 0.254 Chirality : 0.039 0.173 714 Planarity : 0.004 0.036 726 Dihedral : 7.550 59.774 909 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.53 % Allowed : 15.23 % Favored : 81.24 % 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 are not related in a simple way. whole: 1.96 (0.36), residues: 536 helix: 2.16 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.82 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.019 0.001 PHE A 460 TRP 0.009 0.001 TRP A 225 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4551) covalent geometry : angle 0.50946 / 0.25 ( 6233) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 0.31867 / 0.18 ( 2) hydrogen bonds : bond 0.04459 / 2.88 ( 290) hydrogen bonds : angle 4.59954 / 3.19 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.135 Fit side-chains REVERT: A 133 TYR cc_start: 0.8018 (m-10) cc_final: 0.7657 (m-10) REVERT: A 385 SER cc_start: 0.9316 (t) cc_final: 0.9028 (t) REVERT: A 413 ASP cc_start: 0.8257 (m-30) cc_final: 0.7615 (m-30) REVERT: A 525 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: A 549 MET cc_start: 0.8423 (mtt) cc_final: 0.8192 (mtp) REVERT: A 569 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8117 (mm) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.0402 time to fit residues: 5.2710 Evaluate side-chains 94 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127547 restraints weight = 5529.626| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.81 r_work: 0.3389 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4552 Z= 0.175 Angle : 0.544 5.479 6235 Z= 0.270 Chirality : 0.041 0.163 714 Planarity : 0.004 0.035 726 Dihedral : 7.585 59.738 909 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.19 % Allowed : 15.67 % Favored : 80.13 % 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 are not related in a simple way. whole: 1.91 (0.36), residues: 536 helix: 2.10 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.74 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.019 0.001 PHE A 91 TRP 0.010 0.001 TRP A 225 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 4551) covalent geometry : angle 0.54393 / 0.27 ( 6233) SS BOND : bond 0.00447 / 0.24 ( 1) SS BOND : angle 0.83646 / 0.45 ( 2) hydrogen bonds : bond 0.04657 / 3.01 ( 290) hydrogen bonds : angle 4.67830 / 3.24 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8075 (m-10) cc_final: 0.7647 (m-10) REVERT: A 385 SER cc_start: 0.9327 (t) cc_final: 0.9029 (t) REVERT: A 413 ASP cc_start: 0.8266 (m-30) cc_final: 0.7605 (m-30) REVERT: A 414 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: A 525 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8284 (pt0) REVERT: A 569 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8109 (mm) outliers start: 19 outliers final: 15 residues processed: 94 average time/residue: 0.0397 time to fit residues: 5.2390 Evaluate side-chains 97 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114573 restraints weight = 5457.341| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.68 r_work: 0.3190 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4552 Z= 0.146 Angle : 0.519 5.836 6235 Z= 0.259 Chirality : 0.040 0.149 714 Planarity : 0.004 0.035 726 Dihedral : 7.481 59.728 909 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.75 % Allowed : 16.56 % Favored : 79.69 % 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 are not related in a simple way. whole: 2.00 (0.36), residues: 536 helix: 2.15 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.016 0.001 TYR A 132 PHE 0.032 0.001 PHE A 460 TRP 0.009 0.001 TRP A 109 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4551) covalent geometry : angle 0.51918 / 0.26 ( 6233) SS BOND : bond 0.00334 / 0.18 ( 1) SS BOND : angle 0.65428 / 0.36 ( 2) hydrogen bonds : bond 0.04510 / 2.92 ( 290) hydrogen bonds : angle 4.61729 / 3.20 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8038 (m-10) cc_final: 0.7649 (m-10) REVERT: A 385 SER cc_start: 0.9299 (t) cc_final: 0.8983 (t) REVERT: A 413 ASP cc_start: 0.8300 (m-30) cc_final: 0.7728 (m-30) REVERT: A 525 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: A 569 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8170 (mm) outliers start: 17 outliers final: 14 residues processed: 91 average time/residue: 0.0386 time to fit residues: 4.9319 Evaluate side-chains 94 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117867 restraints weight = 5383.548| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.67 r_work: 0.3199 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4552 Z= 0.132 Angle : 0.509 6.116 6235 Z= 0.253 Chirality : 0.039 0.131 714 Planarity : 0.004 0.035 726 Dihedral : 7.369 59.709 909 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.53 % Allowed : 17.22 % Favored : 79.25 % 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 are not related in a simple way. whole: 2.08 (0.36), residues: 536 helix: 2.21 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.64 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.016 0.001 TYR A 132 PHE 0.046 0.001 PHE A 460 TRP 0.009 0.001 TRP A 109 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 4551) covalent geometry : angle 0.50858 / 0.25 ( 6233) SS BOND : bond 0.00176 / 0.09 ( 1) SS BOND : angle 0.44188 / 0.24 ( 2) hydrogen bonds : bond 0.04327 / 2.80 ( 290) hydrogen bonds : angle 4.54809 / 3.15 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8024 (m-10) cc_final: 0.7689 (m-10) REVERT: A 135 MET cc_start: 0.8717 (tpt) cc_final: 0.8024 (tpt) REVERT: A 385 SER cc_start: 0.9287 (t) cc_final: 0.8976 (t) REVERT: A 413 ASP cc_start: 0.8332 (m-30) cc_final: 0.7757 (m-30) REVERT: A 549 MET cc_start: 0.8294 (mtp) cc_final: 0.8022 (mtt) REVERT: A 569 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8163 (mm) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.0397 time to fit residues: 5.0472 Evaluate side-chains 94 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.0050 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116669 restraints weight = 5475.311| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.68 r_work: 0.3215 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4552 Z= 0.122 Angle : 0.512 6.500 6235 Z= 0.253 Chirality : 0.039 0.238 714 Planarity : 0.004 0.034 726 Dihedral : 7.292 59.141 909 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.53 % Allowed : 16.78 % Favored : 79.69 % 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 are not related in a simple way. whole: 2.08 (0.36), residues: 536 helix: 2.20 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.63 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.016 0.001 TYR A 132 PHE 0.024 0.001 PHE A 91 TRP 0.009 0.001 TRP A 109 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 4551) covalent geometry : angle 0.51167 / 0.25 ( 6233) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 0.37533 / 0.20 ( 2) hydrogen bonds : bond 0.04262 / 2.75 ( 290) hydrogen bonds : angle 4.52422 / 3.14 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.7995 (m-10) cc_final: 0.7669 (m-10) REVERT: A 135 MET cc_start: 0.8718 (tpt) cc_final: 0.8024 (tpt) REVERT: A 385 SER cc_start: 0.9281 (t) cc_final: 0.8967 (t) REVERT: A 413 ASP cc_start: 0.8332 (m-30) cc_final: 0.7735 (m-30) REVERT: A 414 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: A 549 MET cc_start: 0.8308 (mtp) cc_final: 0.8028 (mtt) REVERT: A 569 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8130 (mm) outliers start: 16 outliers final: 14 residues processed: 94 average time/residue: 0.0385 time to fit residues: 5.1069 Evaluate side-chains 97 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.117731 restraints weight = 5416.020| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.66 r_work: 0.3193 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4552 Z= 0.112 Angle : 0.500 6.730 6235 Z= 0.247 Chirality : 0.039 0.233 714 Planarity : 0.004 0.034 726 Dihedral : 7.205 59.833 909 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.09 % Allowed : 16.78 % Favored : 80.13 % 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 are not related in a simple way. whole: 2.16 (0.36), residues: 536 helix: 2.26 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.62 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.016 0.001 TYR A 132 PHE 0.015 0.001 PHE A 401 TRP 0.008 0.001 TRP A 160 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4551) covalent geometry : angle 0.50049 / 0.25 ( 6233) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 0.32306 / 0.17 ( 2) hydrogen bonds : bond 0.04083 / 2.63 ( 290) hydrogen bonds : angle 4.48514 / 3.13 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8094 (m-10) cc_final: 0.7741 (m-10) REVERT: A 405 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8078 (pt0) REVERT: A 413 ASP cc_start: 0.8270 (m-30) cc_final: 0.7663 (m-30) REVERT: A 414 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: A 437 MET cc_start: 0.9100 (mtp) cc_final: 0.8887 (mtm) REVERT: A 549 MET cc_start: 0.8238 (mtp) cc_final: 0.7948 (mtt) REVERT: A 569 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8119 (mm) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.0449 time to fit residues: 5.9104 Evaluate side-chains 96 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 569 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.0270 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119623 restraints weight = 5395.284| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.68 r_work: 0.3226 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4552 Z= 0.116 Angle : 0.505 6.568 6235 Z= 0.249 Chirality : 0.039 0.227 714 Planarity : 0.004 0.034 726 Dihedral : 7.140 59.962 909 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.53 % Allowed : 17.00 % Favored : 79.47 % 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 are not related in a simple way. whole: 2.17 (0.36), residues: 536 helix: 2.26 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.57 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.018 0.001 TYR A 132 PHE 0.016 0.001 PHE A 401 TRP 0.009 0.001 TRP A 109 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 4551) covalent geometry : angle 0.50507 / 0.25 ( 6233) SS BOND : bond 0.00098 / 0.05 ( 1) SS BOND : angle 0.36015 / 0.19 ( 2) hydrogen bonds : bond 0.04096 / 2.64 ( 290) hydrogen bonds : angle 4.47082 / 3.11 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1023.65 seconds wall clock time: 18 minutes 13.38 seconds (1093.38 seconds total)