Starting phenix.real_space_refine on Wed Mar 5 15:11:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x64_38079/03_2025/8x64_38079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x64_38079/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x64_38079/03_2025/8x64_38079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x64_38079/03_2025/8x64_38079.map" model { file = "/net/cci-nas-00/data/ceres_data/8x64_38079/03_2025/8x64_38079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x64_38079/03_2025/8x64_38079.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.08, per 1000 atoms: 0.95 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: 0.56 Conformation dependent library (CDL) restraints added in 249.1 milliseconds 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: 0.17 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: 0.52 Time building geometry restraints manager: 0.67 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: 0.820 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.030 ------------------------------------------------------------------------------- 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 2251 Z= 0.385 Angle : 0.789 8.277 3054 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.002 TRP B 455 HIS 0.003 0.001 HIS B 450 PHE 0.010 0.001 PHE B 435 TYR 0.018 0.001 TYR B 200 ARG 0.004 0.000 ARG B 134 *********************** 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 : 0.247 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1426 time to fit residues: 7.3397 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 : 0.248 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 = 0.4757 r_free = 0.4757 target = 0.252500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.222236 restraints weight = 2772.733| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 3.31 r_work: 0.4338 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2251 Z= 0.225 Angle : 0.659 7.450 3054 Z= 0.334 Chirality : 0.041 0.125 349 Planarity : 0.005 0.041 358 Dihedral : 5.577 50.887 299 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.67 % Allowed : 14.23 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.53), residues: 255 helix: 0.95 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -3.52 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.012 0.001 PHE B 435 TYR 0.010 0.001 TYR B 126 ARG 0.001 0.000 ARG B 411 *********************** 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 40 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.233 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1346 time to fit residues: 6.1933 Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 467 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.227665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.200226 restraints weight = 2955.068| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.20 r_work: 0.4227 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2251 Z= 0.255 Angle : 0.680 7.296 3054 Z= 0.347 Chirality : 0.042 0.139 349 Planarity : 0.005 0.042 358 Dihedral : 5.647 48.757 299 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.35 % Allowed : 17.15 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.53), residues: 255 helix: 0.99 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -3.59 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.013 0.001 PHE B 435 TYR 0.012 0.002 TYR B 126 ARG 0.002 0.000 ARG B 411 *********************** 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: 8 poor density : 35 time to evaluate : 0.274 Fit side-chains REVERT: B 206 MET cc_start: 0.4695 (ttm) cc_final: 0.4488 (ttm) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.1449 time to fit residues: 7.2198 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 : 0.253 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.225685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.199346 restraints weight = 2813.912| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 3.05 r_work: 0.4226 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2251 Z= 0.257 Angle : 0.675 7.169 3054 Z= 0.344 Chirality : 0.043 0.143 349 Planarity : 0.005 0.040 358 Dihedral : 5.657 48.830 299 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.35 % Allowed : 20.50 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.53), residues: 255 helix: 0.99 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -3.50 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.014 0.001 PHE B 435 TYR 0.011 0.002 TYR B 126 ARG 0.002 0.000 ARG B 127 *********************** 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 45 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.246 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.1375 time to fit residues: 6.6508 Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 221 LEU 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 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4662 r_free = 0.4662 target = 0.236756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.210147 restraints weight = 2690.843| |-----------------------------------------------------------------------------| r_work (start): 0.4428 rms_B_bonded: 2.82 r_work: 0.4277 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5749 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2251 Z= 0.245 Angle : 0.675 7.077 3054 Z= 0.345 Chirality : 0.043 0.145 349 Planarity : 0.005 0.039 358 Dihedral : 5.650 48.930 299 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.60 % Allowed : 20.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.52), residues: 255 helix: 0.97 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -3.29 (0.77), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.016 0.001 PHE B 435 TYR 0.011 0.002 TYR B 126 ARG 0.001 0.000 ARG B 411 *********************** 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 : 0.231 Fit side-chains REVERT: B 428 TRP cc_start: 0.7266 (OUTLIER) cc_final: 0.6859 (m-10) REVERT: B 454 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6808 (mt) outliers start: 11 outliers final: 5 residues processed: 46 average time/residue: 0.1235 time to fit residues: 6.9265 Evaluate side-chains 45 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.4604 r_free = 0.4604 target = 0.229406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.202903 restraints weight = 2812.509| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 3.07 r_work: 0.4243 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2251 Z= 0.207 Angle : 0.667 11.154 3054 Z= 0.331 Chirality : 0.041 0.180 349 Planarity : 0.004 0.038 358 Dihedral : 5.503 49.018 299 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.18 % Allowed : 21.34 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.53), residues: 255 helix: 0.95 (0.36), residues: 199 sheet: None (None), residues: 0 loop : -3.39 (0.77), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 455 HIS 0.001 0.001 HIS B 59 PHE 0.013 0.001 PHE B 435 TYR 0.008 0.001 TYR B 126 ARG 0.001 0.000 ARG B 134 *********************** 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 46 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.220 Fit side-chains REVERT: B 428 TRP cc_start: 0.7191 (OUTLIER) cc_final: 0.6843 (m-10) REVERT: B 454 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6730 (mt) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.1409 time to fit residues: 7.1189 Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 454 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.233702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.206532 restraints weight = 2677.915| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.87 r_work: 0.4253 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2251 Z= 0.261 Angle : 0.710 10.977 3054 Z= 0.356 Chirality : 0.043 0.165 349 Planarity : 0.005 0.038 358 Dihedral : 5.664 50.080 299 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.02 % Allowed : 20.92 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.52), residues: 255 helix: 0.86 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -3.42 (0.76), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.018 0.001 PHE B 190 TYR 0.012 0.002 TYR B 126 ARG 0.001 0.000 ARG B 411 *********************** 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 48 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: B 428 TRP cc_start: 0.7410 (OUTLIER) cc_final: 0.7012 (m-10) REVERT: B 454 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6838 (mt) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.1518 time to fit residues: 7.8820 Evaluate side-chains 45 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 454 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.2980 chunk 25 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.4594 r_free = 0.4594 target = 0.228744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.201816 restraints weight = 2990.795| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.23 r_work: 0.4202 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2251 Z= 0.206 Angle : 0.664 11.318 3054 Z= 0.329 Chirality : 0.041 0.167 349 Planarity : 0.005 0.037 358 Dihedral : 5.517 49.991 299 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.77 % Allowed : 22.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.53), residues: 255 helix: 1.00 (0.36), residues: 197 sheet: None (None), residues: 0 loop : -3.26 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 455 HIS 0.001 0.001 HIS B 59 PHE 0.013 0.001 PHE B 435 TYR 0.009 0.001 TYR B 126 ARG 0.002 0.000 ARG B 409 *********************** 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 46 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: B 428 TRP cc_start: 0.7261 (OUTLIER) cc_final: 0.6904 (m-10) REVERT: B 454 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6833 (mt) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.1276 time to fit residues: 6.5668 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 : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4617 r_free = 0.4617 target = 0.231438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.203468 restraints weight = 2722.534| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.93 r_work: 0.4160 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2251 Z= 0.283 Angle : 0.719 10.776 3054 Z= 0.363 Chirality : 0.043 0.145 349 Planarity : 0.005 0.037 358 Dihedral : 5.718 50.195 299 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.02 % Allowed : 21.76 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.52), residues: 255 helix: 0.77 (0.35), residues: 197 sheet: None (None), residues: 0 loop : -3.34 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.016 0.001 PHE B 435 TYR 0.013 0.002 TYR B 126 ARG 0.002 0.000 ARG B 411 *********************** 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 50 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: B 428 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.6972 (m-10) REVERT: B 454 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6857 (mt) outliers start: 12 outliers final: 9 residues processed: 46 average time/residue: 0.1466 time to fit residues: 7.9871 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 : 0.241 ------------------------------------------------------------------------------- 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 204 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.4658 r_free = 0.4658 target = 0.237299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.210042 restraints weight = 2653.273| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.88 r_work: 0.4281 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2251 Z= 0.212 Angle : 0.668 10.211 3054 Z= 0.334 Chirality : 0.042 0.157 349 Planarity : 0.005 0.036 358 Dihedral : 5.554 50.147 299 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.18 % Allowed : 22.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.52), residues: 255 helix: 0.94 (0.36), residues: 197 sheet: None (None), residues: 0 loop : -3.27 (0.76), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 455 HIS 0.001 0.001 HIS B 59 PHE 0.015 0.001 PHE B 435 TYR 0.009 0.001 TYR B 126 ARG 0.002 0.000 ARG B 409 ********************** 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 44 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: B 428 TRP cc_start: 0.7207 (OUTLIER) cc_final: 0.6819 (m-10) REVERT: B 454 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6892 (mt) outliers start: 10 outliers final: 7 residues processed: 41 average time/residue: 0.1369 time to fit residues: 6.7415 Evaluate side-chains 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 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 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 = 0.4631 r_free = 0.4631 target = 0.233217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.205497 restraints weight = 2699.076| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.91 r_work: 0.4180 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2251 Z= 0.253 Angle : 0.719 11.862 3054 Z= 0.357 Chirality : 0.043 0.166 349 Planarity : 0.005 0.037 358 Dihedral : 5.622 50.275 299 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.60 % Allowed : 21.34 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.52), residues: 255 helix: 0.83 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -3.44 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.015 0.001 PHE B 435 TYR 0.012 0.002 TYR B 126 ARG 0.002 0.000 ARG B 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1495.34 seconds wall clock time: 26 minutes 29.51 seconds (1589.51 seconds total)