Starting phenix.real_space_refine on Sat Apr 4 22:04:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmo_66099/04_2026/9wmo_66099_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmo_66099/04_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_66099/04_2026/9wmo_66099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmo_66099/04_2026/9wmo_66099.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmo_66099/04_2026/9wmo_66099_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmo_66099/04_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-2.1rc1-6017/lib/python3.9/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, 142 Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 1.18, per 1000 atoms: 0.27 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: 0.27 Conformation dependent library (CDL) restraints added in 212.7 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: 0.08 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: 0.59 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 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 2.470 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 2.470 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.790 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 covalent geometry : bond 0.00530 ( 4551) covalent geometry : angle 0.84632 ( 6233) SS BOND : bond 0.00293 ( 1) SS BOND : angle 0.51859 ( 2) hydrogen bonds : bond 0.12732 ( 290) hydrogen bonds : angle 6.03806 ( 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 : 0.165 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: 0.0782 time to fit residues: 12.8325 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 : 0.149 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 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... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.150257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131777 restraints weight = 5278.879| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.80 r_work: 0.3438 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4552 Z= 0.171 Angle : 0.605 7.701 6235 Z= 0.296 Chirality : 0.040 0.150 714 Planarity : 0.005 0.049 726 Dihedral : 8.507 59.752 909 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.53 % Allowed : 16.11 % 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: 1.44 (0.35), residues: 536 helix: 1.81 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.12 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 420 TYR 0.018 0.002 TYR A 132 PHE 0.014 0.001 PHE A 91 TRP 0.014 0.001 TRP A 215 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 4551) covalent geometry : angle 0.60517 ( 6233) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.17389 ( 2) hydrogen bonds : bond 0.04891 ( 290) hydrogen bonds : angle 4.81417 ( 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 104 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.186 Fit side-chains REVERT: A 133 TYR cc_start: 0.8071 (m-10) cc_final: 0.7644 (m-10) REVERT: A 351 GLU cc_start: 0.8367 (tp30) cc_final: 0.8020 (tp30) REVERT: A 385 SER cc_start: 0.9203 (t) cc_final: 0.8918 (t) REVERT: A 413 ASP cc_start: 0.8204 (m-30) cc_final: 0.7690 (m-30) REVERT: A 525 GLU cc_start: 0.8274 (pt0) cc_final: 0.7952 (mt-10) REVERT: A 545 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7150 (tp) REVERT: A 569 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8110 (mm) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 0.0511 time to fit residues: 6.7911 Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.0040 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128520 restraints weight = 5179.225| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.81 r_work: 0.3364 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2392 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= 0.130 Angle : 0.510 5.360 6235 Z= 0.256 Chirality : 0.038 0.137 714 Planarity : 0.004 0.042 726 Dihedral : 7.521 58.506 909 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.97 % Allowed : 13.91 % Favored : 82.12 % 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 are not related in a simple way. whole: 1.95 (0.36), residues: 536 helix: 2.17 (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 0.009 0.001 ARG A 560 TYR 0.015 0.001 TYR A 132 PHE 0.016 0.001 PHE A 460 TRP 0.008 0.001 TRP A 225 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4551) covalent geometry : angle 0.51021 ( 6233) SS BOND : bond 0.00682 ( 1) SS BOND : angle 0.97370 ( 2) hydrogen bonds : bond 0.04471 ( 290) hydrogen bonds : angle 4.58982 ( 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 107 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.7968 (m-10) cc_final: 0.7549 (m-10) REVERT: A 150 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8443 (m) REVERT: A 234 LYS cc_start: 0.8062 (tppt) cc_final: 0.6938 (tmtt) REVERT: A 286 LYS cc_start: 0.8540 (tttt) cc_final: 0.8133 (ttpp) REVERT: A 385 SER cc_start: 0.9220 (t) cc_final: 0.8924 (t) REVERT: A 413 ASP cc_start: 0.8224 (m-30) cc_final: 0.7732 (m-30) REVERT: A 422 LYS cc_start: 0.7852 (mttp) cc_final: 0.7547 (mttt) REVERT: A 569 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8021 (mm) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 0.0654 time to fit residues: 8.5477 Evaluate side-chains 97 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122044 restraints weight = 5247.108| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.84 r_work: 0.3301 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2580 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= 0.163 Angle : 0.545 7.844 6235 Z= 0.268 Chirality : 0.040 0.135 714 Planarity : 0.004 0.036 726 Dihedral : 7.680 55.349 909 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.53 % Allowed : 14.13 % 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: 1.85 (0.36), residues: 536 helix: 2.07 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.83 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.015 0.001 TYR A 132 PHE 0.017 0.001 PHE A 91 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 4551) covalent geometry : angle 0.54550 ( 6233) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.44383 ( 2) hydrogen bonds : bond 0.04685 ( 290) hydrogen bonds : angle 4.64530 ( 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 : 0.182 Fit side-chains REVERT: A 133 TYR cc_start: 0.8023 (m-10) cc_final: 0.7623 (m-10) REVERT: A 357 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8438 (p0) REVERT: A 385 SER cc_start: 0.9291 (t) cc_final: 0.8981 (t) REVERT: A 413 ASP cc_start: 0.8198 (m-30) cc_final: 0.7603 (m-30) REVERT: A 569 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7930 (mm) REVERT: A 584 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7757 (mt-10) outliers start: 16 outliers final: 12 residues processed: 91 average time/residue: 0.0446 time to fit residues: 5.6940 Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 357 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 558 VAL 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 584 GLU 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: 0.8980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117106 restraints weight = 5421.217| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.67 r_work: 0.3090 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4552 Z= 0.130 Angle : 0.499 5.304 6235 Z= 0.249 Chirality : 0.038 0.133 714 Planarity : 0.004 0.036 726 Dihedral : 7.557 57.336 909 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.87 % Allowed : 15.89 % 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: 2.06 (0.36), residues: 536 helix: 2.21 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.69 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.016 0.001 TYR A 132 PHE 0.018 0.001 PHE A 460 TRP 0.008 0.001 TRP A 109 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4551) covalent geometry : angle 0.49883 ( 6233) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.99474 ( 2) hydrogen bonds : bond 0.04412 ( 290) hydrogen bonds : angle 4.52718 ( 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 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.7909 (m-10) cc_final: 0.7491 (m-10) REVERT: A 357 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8366 (p0) REVERT: A 385 SER cc_start: 0.9310 (t) cc_final: 0.9001 (t) REVERT: A 413 ASP cc_start: 0.8151 (m-30) cc_final: 0.7560 (m-30) REVERT: A 569 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8073 (mm) outliers start: 13 outliers final: 11 residues processed: 86 average time/residue: 0.0493 time to fit residues: 5.9857 Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 357 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 544 LEU 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: 0.6980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115669 restraints weight = 5606.856| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.71 r_work: 0.3136 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2871 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= 0.146 Angle : 0.515 5.431 6235 Z= 0.257 Chirality : 0.039 0.131 714 Planarity : 0.004 0.035 726 Dihedral : 7.515 59.218 909 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.53 % Allowed : 16.56 % Favored : 79.91 % 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: 2.04 (0.36), residues: 536 helix: 2.17 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.66 (0.48), residues: 160 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 0.009 0.001 TRP A 225 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4551) covalent geometry : angle 0.51443 ( 6233) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.83526 ( 2) hydrogen bonds : bond 0.04470 ( 290) hydrogen bonds : angle 4.56791 ( 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 96 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.7993 (m-10) cc_final: 0.7592 (m-10) REVERT: A 385 SER cc_start: 0.9335 (t) cc_final: 0.9024 (t) REVERT: A 413 ASP cc_start: 0.8241 (m-30) cc_final: 0.7643 (m-30) REVERT: A 525 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: A 569 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8163 (mm) outliers start: 16 outliers final: 10 residues processed: 89 average time/residue: 0.0478 time to fit residues: 6.0309 Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0870 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126753 restraints weight = 5352.886| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.88 r_work: 0.3354 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2997 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= 0.121 Angle : 0.487 5.772 6235 Z= 0.243 Chirality : 0.038 0.127 714 Planarity : 0.004 0.035 726 Dihedral : 7.378 58.252 909 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.87 % Allowed : 17.44 % 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: 2.18 (0.36), residues: 536 helix: 2.27 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.58 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.015 0.001 TYR A 132 PHE 0.031 0.001 PHE A 460 TRP 0.008 0.001 TRP A 109 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4551) covalent geometry : angle 0.48697 ( 6233) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.80533 ( 2) hydrogen bonds : bond 0.04230 ( 290) hydrogen bonds : angle 4.46716 ( 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 95 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.7999 (m-10) cc_final: 0.7637 (m-10) REVERT: A 135 MET cc_start: 0.8723 (tpt) cc_final: 0.7996 (tpt) REVERT: A 385 SER cc_start: 0.9305 (t) cc_final: 0.9016 (t) REVERT: A 413 ASP cc_start: 0.8241 (m-30) cc_final: 0.7640 (m-30) REVERT: A 569 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8119 (mm) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.0477 time to fit residues: 6.1689 Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.0030 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131235 restraints weight = 5289.419| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.82 r_work: 0.3407 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4552 Z= 0.118 Angle : 0.495 6.118 6235 Z= 0.246 Chirality : 0.038 0.194 714 Planarity : 0.004 0.034 726 Dihedral : 7.269 57.097 909 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.87 % Allowed : 17.44 % 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: 2.20 (0.36), residues: 536 helix: 2.28 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.56 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.015 0.001 TYR A 132 PHE 0.045 0.001 PHE A 460 TRP 0.008 0.001 TRP A 109 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4551) covalent geometry : angle 0.49476 ( 6233) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.76036 ( 2) hydrogen bonds : bond 0.04174 ( 290) hydrogen bonds : angle 4.47312 ( 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 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8000 (m-10) cc_final: 0.7665 (m-10) REVERT: A 135 MET cc_start: 0.8722 (tpt) cc_final: 0.8074 (tpt) REVERT: A 413 ASP cc_start: 0.8214 (m-30) cc_final: 0.7543 (m-30) REVERT: A 414 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: A 569 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8125 (mm) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.0482 time to fit residues: 5.9661 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 : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 0.0670 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131951 restraints weight = 5317.056| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.82 r_work: 0.3439 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3186 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 : 0.490 6.211 6235 Z= 0.242 Chirality : 0.038 0.206 714 Planarity : 0.004 0.034 726 Dihedral : 7.147 55.995 909 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.43 % Allowed : 17.66 % Favored : 79.91 % 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: 2.19 (0.36), residues: 536 helix: 2.27 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.56 (0.48), residues: 160 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 0.017 0.001 PHE A 91 TRP 0.008 0.001 TRP A 109 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4551) covalent geometry : angle 0.48996 ( 6233) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.69936 ( 2) hydrogen bonds : bond 0.04037 ( 290) hydrogen bonds : angle 4.41551 ( 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 90 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8086 (m-10) cc_final: 0.7745 (m-10) REVERT: A 405 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8041 (pt0) REVERT: A 413 ASP cc_start: 0.8264 (m-30) cc_final: 0.7670 (m-30) REVERT: A 437 MET cc_start: 0.9107 (mtp) cc_final: 0.8879 (mtm) REVERT: A 569 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8127 (mm) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.0500 time to fit residues: 6.0441 Evaluate side-chains 89 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU 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 436 LEU Chi-restraints excluded: chain A residue 544 LEU 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 47 optimal weight: 0.0020 chunk 3 optimal weight: 0.0470 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133251 restraints weight = 5284.672| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.81 r_work: 0.3462 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4552 Z= 0.107 Angle : 0.488 6.459 6235 Z= 0.240 Chirality : 0.038 0.202 714 Planarity : 0.004 0.034 726 Dihedral : 7.049 55.634 909 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 17.88 % Favored : 79.91 % 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: 2.23 (0.36), residues: 536 helix: 2.29 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.54 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.014 0.001 TYR A 132 PHE 0.017 0.001 PHE A 91 TRP 0.008 0.001 TRP A 109 HIS 0.008 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4551) covalent geometry : angle 0.48808 ( 6233) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.63042 ( 2) hydrogen bonds : bond 0.03973 ( 290) hydrogen bonds : angle 4.36542 ( 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 89 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8031 (m-10) cc_final: 0.7733 (m-10) REVERT: A 135 MET cc_start: 0.8742 (tpt) cc_final: 0.8119 (tpt) REVERT: A 405 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8052 (pt0) REVERT: A 413 ASP cc_start: 0.8243 (m-30) cc_final: 0.7638 (m-30) REVERT: A 437 MET cc_start: 0.9118 (mtp) cc_final: 0.8897 (mtm) REVERT: A 569 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8129 (mm) outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 0.0497 time to fit residues: 5.9455 Evaluate side-chains 88 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU 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 349 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 LEU 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: 0.5980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.0000 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.0170 overall best weight: 0.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132755 restraints weight = 5313.999| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.82 r_work: 0.3455 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3266 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= 0.109 Angle : 0.486 6.584 6235 Z= 0.240 Chirality : 0.038 0.201 714 Planarity : 0.004 0.034 726 Dihedral : 6.965 58.109 909 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.65 % Allowed : 17.44 % Favored : 79.91 % 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: 2.29 (0.36), residues: 536 helix: 2.33 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.47 (0.49), residues: 159 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 0.015 0.001 PHE A 401 TRP 0.008 0.001 TRP A 109 HIS 0.008 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4551) covalent geometry : angle 0.48636 ( 6233) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.57225 ( 2) hydrogen bonds : bond 0.03956 ( 290) hydrogen bonds : angle 4.34052 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.05 seconds wall clock time: 21 minutes 11.89 seconds (1271.89 seconds total)