Starting phenix.real_space_refine on Fri Aug 22 12:38:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x64_38079/08_2025/8x64_38079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x64_38079/08_2025/8x64_38079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x64_38079/08_2025/8x64_38079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x64_38079/08_2025/8x64_38079.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x64_38079/08_2025/8x64_38079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x64_38079/08_2025/8x64_38079.map" } resolution = 3.4 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= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 1472 2.51 5 N 351 2.21 5 O 345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2189 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2167 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 3 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y5R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.46 Number of scatterers: 2189 At special positions: 0 Unit cell: (54.06, 73.14, 71.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 345 8.00 N 351 7.00 C 1472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " 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: 0.20 Conformation dependent library (CDL) restraints added in 80.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 81.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.669A pdb=" N CYS B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 removed outlier: 3.909A pdb=" N ILE B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 96 through 130 removed outlier: 3.825A pdb=" N CYS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 187 through 220 removed outlier: 3.509A pdb=" N LYS B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 439 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 447 through 472 removed outlier: 3.644A pdb=" N MET B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix Processing helix chain 'B' and resid 475 through 480 151 hydrogen bonds defined for protein. 453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 305 1.30 - 1.43: 644 1.43 - 1.56: 1268 1.56 - 1.68: 2 1.68 - 1.81: 32 Bond restraints: 2251 Sorted by residual: bond pdb=" C PHE B 424 " pdb=" N ILE B 425 " ideal model delta sigma weight residual 1.332 1.257 0.075 1.36e-02 5.41e+03 3.04e+01 bond pdb=" C PHE B 424 " pdb=" O PHE B 424 " ideal model delta sigma weight residual 1.235 1.172 0.064 1.26e-02 6.30e+03 2.55e+01 bond pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta sigma weight residual 1.530 1.447 0.084 1.69e-02 3.50e+03 2.44e+01 bond pdb=" CA PHE B 424 " pdb=" C PHE B 424 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.34e-02 5.57e+03 2.32e+01 bond pdb=" N PHE B 424 " pdb=" CA PHE B 424 " ideal model delta sigma weight residual 1.457 1.396 0.061 1.29e-02 6.01e+03 2.27e+01 ... (remaining 2246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 2924 1.66 - 3.31: 94 3.31 - 4.97: 25 4.97 - 6.62: 8 6.62 - 8.28: 3 Bond angle restraints: 3054 Sorted by residual: angle pdb=" CA ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 117.30 124.60 -7.30 1.16e+00 7.43e-01 3.96e+01 angle pdb=" O ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 122.12 116.20 5.92 1.06e+00 8.90e-01 3.12e+01 angle pdb=" N PHE B 424 " pdb=" CA PHE B 424 " pdb=" C PHE B 424 " ideal model delta sigma weight residual 110.80 102.52 8.28 2.13e+00 2.20e-01 1.51e+01 angle pdb=" CA ILE B 115 " pdb=" C ILE B 115 " pdb=" N PHE B 116 " ideal model delta sigma weight residual 116.60 121.79 -5.19 1.45e+00 4.76e-01 1.28e+01 angle pdb=" N ALA B 423 " pdb=" CA ALA B 423 " pdb=" C ALA B 423 " ideal model delta sigma weight residual 111.28 114.76 -3.48 1.09e+00 8.42e-01 1.02e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 1116 14.25 - 28.50: 145 28.50 - 42.74: 52 42.74 - 56.99: 7 56.99 - 71.24: 1 Dihedral angle restraints: 1321 sinusoidal: 538 harmonic: 783 Sorted by residual: dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -142.50 56.50 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" C ILE B 115 " pdb=" N ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta harmonic sigma weight residual -122.00 -134.73 12.73 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta harmonic sigma weight residual 123.40 135.77 -12.37 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 1318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 328 0.085 - 0.169: 20 0.169 - 0.254: 0 0.254 - 0.339: 0 0.339 - 0.423: 1 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA MET B 81 " pdb=" N MET B 81 " pdb=" C MET B 81 " pdb=" CB MET B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CB ILE B 115 " pdb=" CA ILE B 115 " pdb=" CG1 ILE B 115 " pdb=" CG2 ILE B 115 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 346 not shown) Planarity restraints: 358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 424 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PHE B 424 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE B 424 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE B 425 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C SER B 114 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 114 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 115 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 78 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ALA B 78 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA B 78 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 79 " -0.015 2.00e-02 2.50e+03 ... (remaining 355 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 609 2.81 - 3.33: 2228 3.33 - 3.86: 3460 3.86 - 4.38: 3778 4.38 - 4.90: 6258 Nonbonded interactions: 16333 Sorted by model distance: nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP B 73 " pdb=" OG SER B 461 " model vdw 2.296 3.040 nonbonded pdb=" O PHE B 424 " pdb=" C ILE B 425 " model vdw 2.317 3.270 nonbonded pdb=" O ALA B 423 " pdb=" ND2 ASN B 460 " model vdw 2.380 3.120 nonbonded pdb=" OH TYR B 214 " pdb=" NZ LYS B 218 " model vdw 2.384 3.120 ... (remaining 16328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.670 Set stop_for_unknowns flag: 0.010 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.710 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:1.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 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 : 0.006 0.084 2253 Z= 0.358 Angle : 0.789 8.277 3058 Z= 0.428 Chirality : 0.048 0.423 349 Planarity : 0.007 0.047 358 Dihedral : 14.113 71.238 805 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.42 % Allowed : 0.00 % Favored : 99.58 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.53), residues: 255 helix: 0.47 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -3.69 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.018 0.001 TYR B 200 PHE 0.010 0.001 PHE B 435 TRP 0.030 0.002 TRP B 455 HIS 0.003 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 2251) covalent geometry : angle 0.78918 ( 3054) SS BOND : bond 0.00082 ( 2) SS BOND : angle 0.64590 ( 4) hydrogen bonds : bond 0.11981 ( 151) hydrogen bonds : angle 6.27632 ( 453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.098 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.0635 time to fit residues: 3.2600 Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 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 = 0.4728 r_free = 0.4728 target = 0.249329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.218890 restraints weight = 2849.161| |-----------------------------------------------------------------------------| r_work (start): 0.4465 rms_B_bonded: 3.36 r_work: 0.4309 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2253 Z= 0.165 Angle : 0.683 7.468 3058 Z= 0.347 Chirality : 0.042 0.131 349 Planarity : 0.005 0.041 358 Dihedral : 5.668 51.463 299 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.09 % Allowed : 14.23 % Favored : 83.68 % 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 aren not related in a simple way. whole: -0.25 (0.53), residues: 255 helix: 0.84 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -3.57 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 411 TYR 0.011 0.001 TYR B 126 PHE 0.013 0.001 PHE B 435 TRP 0.018 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2251) covalent geometry : angle 0.68280 ( 3054) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.62840 ( 4) hydrogen bonds : bond 0.04365 ( 151) hydrogen bonds : angle 4.82109 ( 453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.084 Fit side-chains REVERT: B 206 MET cc_start: 0.3991 (OUTLIER) cc_final: 0.3787 (ttm) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.0587 time to fit residues: 2.9935 Evaluate side-chains 41 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.231886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.202313 restraints weight = 2890.920| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 3.35 r_work: 0.4203 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2253 Z= 0.174 Angle : 0.680 7.245 3058 Z= 0.349 Chirality : 0.042 0.138 349 Planarity : 0.005 0.041 358 Dihedral : 5.651 48.381 299 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.18 % Allowed : 17.57 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.53), residues: 255 helix: 0.94 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -3.56 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 411 TYR 0.012 0.001 TYR B 126 PHE 0.014 0.001 PHE B 435 TRP 0.012 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 2251) covalent geometry : angle 0.68004 ( 3054) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.63702 ( 4) hydrogen bonds : bond 0.04346 ( 151) hydrogen bonds : angle 4.85922 ( 453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.087 Fit side-chains REVERT: B 206 MET cc_start: 0.4731 (OUTLIER) cc_final: 0.4492 (ttm) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.0617 time to fit residues: 2.9740 Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.0670 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 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 = 0.4690 r_free = 0.4690 target = 0.238483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.211863 restraints weight = 2799.996| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 3.11 r_work: 0.4311 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2253 Z= 0.146 Angle : 0.635 7.119 3058 Z= 0.321 Chirality : 0.041 0.125 349 Planarity : 0.005 0.039 358 Dihedral : 5.506 48.347 299 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.93 % Allowed : 21.34 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.53), residues: 255 helix: 1.11 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -3.41 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 411 TYR 0.009 0.001 TYR B 126 PHE 0.012 0.001 PHE B 435 TRP 0.012 0.001 TRP B 455 HIS 0.001 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2251) covalent geometry : angle 0.63511 ( 3054) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.48610 ( 4) hydrogen bonds : bond 0.04112 ( 151) hydrogen bonds : angle 4.66892 ( 453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.085 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 0.0605 time to fit residues: 2.8467 Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.0060 chunk 18 optimal weight: 0.0370 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.1610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.243731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.217822 restraints weight = 2803.636| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 3.04 r_work: 0.4401 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2253 Z= 0.122 Angle : 0.593 7.006 3058 Z= 0.300 Chirality : 0.040 0.152 349 Planarity : 0.004 0.039 358 Dihedral : 5.240 48.914 299 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.60 % Allowed : 20.08 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.53), residues: 255 helix: 1.39 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -3.23 (0.74), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 411 TYR 0.006 0.001 TYR B 126 PHE 0.013 0.001 PHE B 435 TRP 0.011 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2251) covalent geometry : angle 0.59346 ( 3054) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.32728 ( 4) hydrogen bonds : bond 0.03754 ( 151) hydrogen bonds : angle 4.43294 ( 453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.082 Fit side-chains REVERT: B 428 TRP cc_start: 0.7139 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: B 454 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6755 (mt) outliers start: 11 outliers final: 5 residues processed: 45 average time/residue: 0.0600 time to fit residues: 3.2633 Evaluate side-chains 42 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 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 = 0.4681 r_free = 0.4681 target = 0.236995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.210241 restraints weight = 2714.436| |-----------------------------------------------------------------------------| r_work (start): 0.4465 rms_B_bonded: 2.95 r_work: 0.4324 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2253 Z= 0.151 Angle : 0.662 10.987 3058 Z= 0.331 Chirality : 0.042 0.181 349 Planarity : 0.005 0.039 358 Dihedral : 5.393 49.752 299 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.18 % Allowed : 20.92 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.53), residues: 255 helix: 1.26 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -3.34 (0.73), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 134 TYR 0.012 0.001 TYR B 126 PHE 0.014 0.001 PHE B 435 TRP 0.012 0.001 TRP B 455 HIS 0.001 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 2251) covalent geometry : angle 0.66194 ( 3054) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.40078 ( 4) hydrogen bonds : bond 0.04078 ( 151) hydrogen bonds : angle 4.64694 ( 453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.086 Fit side-chains REVERT: B 428 TRP cc_start: 0.7174 (OUTLIER) cc_final: 0.6786 (m-10) REVERT: B 454 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6755 (mt) outliers start: 10 outliers final: 4 residues processed: 44 average time/residue: 0.0580 time to fit residues: 3.0724 Evaluate side-chains 41 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 chunk 20 optimal weight: 0.6980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.239228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.212387 restraints weight = 2778.628| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 3.07 r_work: 0.4338 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2253 Z= 0.143 Angle : 0.649 10.289 3058 Z= 0.325 Chirality : 0.041 0.161 349 Planarity : 0.004 0.038 358 Dihedral : 5.376 50.027 299 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.02 % Allowed : 21.34 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.53), residues: 255 helix: 1.33 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -3.36 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 411 TYR 0.010 0.001 TYR B 200 PHE 0.014 0.001 PHE B 435 TRP 0.010 0.001 TRP B 455 HIS 0.001 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2251) covalent geometry : angle 0.64897 ( 3054) SS BOND : bond 0.00154 ( 2) SS BOND : angle 0.42429 ( 4) hydrogen bonds : bond 0.03934 ( 151) hydrogen bonds : angle 4.60313 ( 453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.082 Fit side-chains REVERT: B 428 TRP cc_start: 0.7114 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: B 454 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6652 (mt) outliers start: 12 outliers final: 7 residues processed: 40 average time/residue: 0.0587 time to fit residues: 2.8078 Evaluate side-chains 42 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.224132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.197383 restraints weight = 2873.332| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.10 r_work: 0.4162 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2253 Z= 0.175 Angle : 0.707 11.028 3058 Z= 0.354 Chirality : 0.042 0.145 349 Planarity : 0.005 0.038 358 Dihedral : 5.555 50.124 299 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 6.28 % Allowed : 20.92 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.53), residues: 255 helix: 1.01 (0.36), residues: 197 sheet: None (None), residues: 0 loop : -3.29 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.012 0.002 TYR B 126 PHE 0.016 0.001 PHE B 435 TRP 0.010 0.001 TRP B 455 HIS 0.002 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 2251) covalent geometry : angle 0.70745 ( 3054) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.46083 ( 4) hydrogen bonds : bond 0.04271 ( 151) hydrogen bonds : angle 4.81497 ( 453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.084 Fit side-chains REVERT: B 428 TRP cc_start: 0.7199 (OUTLIER) cc_final: 0.6854 (m-10) REVERT: B 454 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6669 (mt) outliers start: 15 outliers final: 11 residues processed: 43 average time/residue: 0.0580 time to fit residues: 3.0097 Evaluate side-chains 47 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.227221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.200681 restraints weight = 2914.986| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 3.13 r_work: 0.4210 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2253 Z= 0.162 Angle : 0.694 10.785 3058 Z= 0.346 Chirality : 0.042 0.156 349 Planarity : 0.005 0.038 358 Dihedral : 5.542 50.202 299 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.44 % Allowed : 22.59 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.53), residues: 255 helix: 0.96 (0.36), residues: 197 sheet: None (None), residues: 0 loop : -3.26 (0.76), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 411 TYR 0.010 0.001 TYR B 126 PHE 0.015 0.001 PHE B 435 TRP 0.010 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 2251) covalent geometry : angle 0.69372 ( 3054) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.52288 ( 4) hydrogen bonds : bond 0.04185 ( 151) hydrogen bonds : angle 4.78316 ( 453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.102 Fit side-chains REVERT: B 428 TRP cc_start: 0.7278 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: B 454 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6843 (mt) outliers start: 13 outliers final: 10 residues processed: 42 average time/residue: 0.0676 time to fit residues: 3.4269 Evaluate side-chains 46 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.0470 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.226421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.199783 restraints weight = 2944.405| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.14 r_work: 0.4186 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2253 Z= 0.170 Angle : 0.700 10.830 3058 Z= 0.350 Chirality : 0.043 0.156 349 Planarity : 0.005 0.038 358 Dihedral : 5.587 50.473 299 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.02 % Allowed : 22.59 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.52), residues: 255 helix: 0.91 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -3.49 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 411 TYR 0.011 0.002 TYR B 126 PHE 0.014 0.001 PHE B 435 TRP 0.010 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 2251) covalent geometry : angle 0.69992 ( 3054) SS BOND : bond 0.00173 ( 2) SS BOND : angle 0.81506 ( 4) hydrogen bonds : bond 0.04228 ( 151) hydrogen bonds : angle 4.81060 ( 453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.086 Fit side-chains REVERT: B 428 TRP cc_start: 0.7227 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: B 454 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6777 (mt) outliers start: 12 outliers final: 10 residues processed: 41 average time/residue: 0.0774 time to fit residues: 3.6719 Evaluate side-chains 46 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 428 TRP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.228538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.201081 restraints weight = 2929.213| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 3.20 r_work: 0.4216 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2253 Z= 0.151 Angle : 0.677 10.747 3058 Z= 0.337 Chirality : 0.042 0.159 349 Planarity : 0.005 0.037 358 Dihedral : 5.520 50.316 299 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.60 % Allowed : 22.59 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.53), residues: 255 helix: 1.01 (0.36), residues: 197 sheet: None (None), residues: 0 loop : -3.38 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.009 0.001 TYR B 126 PHE 0.013 0.001 PHE B 435 TRP 0.010 0.001 TRP B 455 HIS 0.001 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 2251) covalent geometry : angle 0.67733 ( 3054) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.61926 ( 4) hydrogen bonds : bond 0.04140 ( 151) hydrogen bonds : angle 4.72247 ( 453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 824.34 seconds wall clock time: 15 minutes 13.34 seconds (913.34 seconds total)