Starting phenix.real_space_refine on Fri Dec 27 09:28:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wn0_32618/12_2024/7wn0_32618.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wn0_32618/12_2024/7wn0_32618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wn0_32618/12_2024/7wn0_32618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wn0_32618/12_2024/7wn0_32618.map" model { file = "/net/cci-nas-00/data/ceres_data/7wn0_32618/12_2024/7wn0_32618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wn0_32618/12_2024/7wn0_32618.cif" } resolution = 3.64 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= 0.028 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2553 2.51 5 N 617 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3879 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2953 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 926 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Time building chain proxies: 3.03, per 1000 atoms: 0.78 Number of scatterers: 3879 At special positions: 0 Unit cell: (112.05, 57.27, 61.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 683 8.00 N 617 7.00 C 2553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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: 0.99 Conformation dependent library (CDL) restraints added in 446.9 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 61.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 31 through 59 removed outlier: 4.516A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.887A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 Processing helix chain 'A' and resid 112 through 144 Processing helix chain 'A' and resid 149 through 173 removed outlier: 4.389A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 210 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.802A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 3.752A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.284A pdb=" N PHE A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.678A pdb=" N VAL A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.769A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.519A pdb=" N LEU A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Proline residue: A 361 - end of helix removed outlier: 5.247A pdb=" N VAL A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 399 removed outlier: 3.611A pdb=" N GLU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.005A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 406' Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.716A pdb=" N SER B 122 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 33 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.716A pdb=" N SER B 122 " --> pdb=" O VAL B 12 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 753 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: 1.14 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1176 1.34 - 1.46: 999 1.46 - 1.58: 1757 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 3971 Sorted by residual: bond pdb=" N TYR B 103 " pdb=" CA TYR B 103 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.35e-02 5.49e+03 8.72e+00 bond pdb=" CG PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 1.503 1.539 -0.036 3.40e-02 8.65e+02 1.11e+00 bond pdb=" CA VAL B 48 " pdb=" CB VAL B 48 " ideal model delta sigma weight residual 1.545 1.538 0.007 9.10e-03 1.21e+04 6.63e-01 bond pdb=" CB ASP A 333 " pdb=" CG ASP A 333 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.84e-01 bond pdb=" CB LEU A 44 " pdb=" CG LEU A 44 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.74e-01 ... (remaining 3966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 5317 1.91 - 3.83: 56 3.83 - 5.74: 12 5.74 - 7.65: 5 7.65 - 9.56: 1 Bond angle restraints: 5391 Sorted by residual: angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 107.92 4.08 1.40e+00 5.10e-01 8.51e+00 angle pdb=" CA LEU A 201 " pdb=" CB LEU A 201 " pdb=" CG LEU A 201 " ideal model delta sigma weight residual 116.30 125.86 -9.56 3.50e+00 8.16e-02 7.47e+00 angle pdb=" N TYR B 103 " pdb=" CA TYR B 103 " pdb=" C TYR B 103 " ideal model delta sigma weight residual 112.87 110.07 2.80 1.20e+00 6.94e-01 5.43e+00 angle pdb=" CB MET A 233 " pdb=" CG MET A 233 " pdb=" SD MET A 233 " ideal model delta sigma weight residual 112.70 119.59 -6.89 3.00e+00 1.11e-01 5.27e+00 angle pdb=" N SER A 308 " pdb=" CA SER A 308 " pdb=" C SER A 308 " ideal model delta sigma weight residual 107.88 110.66 -2.78 1.41e+00 5.03e-01 3.87e+00 ... (remaining 5386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 1943 17.13 - 34.27: 278 34.27 - 51.40: 74 51.40 - 68.54: 8 68.54 - 85.67: 2 Dihedral angle restraints: 2305 sinusoidal: 875 harmonic: 1430 Sorted by residual: dihedral pdb=" CA HIS A 334 " pdb=" C HIS A 334 " pdb=" N PRO A 335 " pdb=" CA PRO A 335 " ideal model delta harmonic sigma weight residual 180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASN A 148 " pdb=" CB ASN A 148 " pdb=" CG ASN A 148 " pdb=" OD1 ASN A 148 " ideal model delta sinusoidal sigma weight residual -90.00 -163.46 73.46 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CG ARG B 66 " pdb=" CD ARG B 66 " pdb=" NE ARG B 66 " pdb=" CZ ARG B 66 " ideal model delta sinusoidal sigma weight residual -180.00 -135.39 -44.61 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 2302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 354 0.028 - 0.056: 174 0.056 - 0.085: 69 0.085 - 0.113: 27 0.113 - 0.141: 4 Chirality restraints: 628 Sorted by residual: chirality pdb=" CA PRO A 335 " pdb=" N PRO A 335 " pdb=" C PRO A 335 " pdb=" CB PRO A 335 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 625 not shown) Planarity restraints: 663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " -0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO A 258 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 293 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A 294 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 119 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C TYR A 119 " -0.031 2.00e-02 2.50e+03 pdb=" O TYR A 119 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS A 120 " 0.011 2.00e-02 2.50e+03 ... (remaining 660 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1043 2.80 - 3.32: 3846 3.32 - 3.85: 6520 3.85 - 4.37: 7483 4.37 - 4.90: 13006 Nonbonded interactions: 31898 Sorted by model distance: nonbonded pdb=" N GLU B 88 " pdb=" OE1 GLU B 88 " model vdw 2.273 3.120 nonbonded pdb=" N GLU A 146 " pdb=" OE1 GLU A 146 " model vdw 2.275 3.120 nonbonded pdb=" OG1 THR A 253 " pdb=" NH2 ARG A 319 " model vdw 2.284 3.120 nonbonded pdb=" N GLN B 44 " pdb=" OE1 GLN B 44 " model vdw 2.316 3.120 nonbonded pdb=" O SER B 102 " pdb=" OG SER B 102 " model vdw 2.325 3.040 ... (remaining 31893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.003 0.040 3971 Z= 0.199 Angle : 0.572 9.565 5391 Z= 0.296 Chirality : 0.041 0.141 628 Planarity : 0.005 0.098 663 Dihedral : 16.818 85.672 1382 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.47 % Allowed : 28.44 % Favored : 71.10 % 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: 1.10 (0.39), residues: 488 helix: 1.00 (0.32), residues: 278 sheet: 1.61 (0.73), residues: 56 loop : 0.07 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 356 HIS 0.010 0.001 HIS A 334 PHE 0.012 0.001 PHE A 82 TYR 0.015 0.001 TYR A 119 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.1408 time to fit residues: 13.6748 Evaluate side-chains 77 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.0870 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 135 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 284 GLN A 316 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3971 Z= 0.253 Angle : 0.597 8.021 5391 Z= 0.312 Chirality : 0.043 0.129 628 Planarity : 0.005 0.053 663 Dihedral : 4.556 34.698 521 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.66 % Allowed : 25.87 % Favored : 69.46 % 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: 1.36 (0.39), residues: 488 helix: 1.29 (0.31), residues: 285 sheet: 1.16 (0.62), residues: 69 loop : 0.09 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 356 HIS 0.007 0.001 HIS A 334 PHE 0.014 0.001 PHE A 36 TYR 0.014 0.002 TYR A 119 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6410 (mt) REVERT: A 349 MET cc_start: 0.6715 (tpt) cc_final: 0.6074 (mtp) REVERT: B 55 ASP cc_start: 0.8283 (t0) cc_final: 0.7983 (t0) outliers start: 20 outliers final: 13 residues processed: 89 average time/residue: 0.1399 time to fit residues: 15.8714 Evaluate side-chains 89 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.0170 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3971 Z= 0.191 Angle : 0.557 7.902 5391 Z= 0.287 Chirality : 0.041 0.122 628 Planarity : 0.004 0.051 663 Dihedral : 4.154 33.230 519 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.90 % Allowed : 26.11 % Favored : 69.00 % 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: 1.52 (0.39), residues: 488 helix: 1.52 (0.31), residues: 285 sheet: 1.03 (0.58), residues: 69 loop : 0.03 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 356 HIS 0.006 0.001 HIS A 334 PHE 0.007 0.001 PHE A 365 TYR 0.019 0.001 TYR B 37 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 349 MET cc_start: 0.6734 (tpt) cc_final: 0.6094 (mtp) REVERT: A 389 MET cc_start: 0.9066 (ttp) cc_final: 0.8824 (ttt) REVERT: B 37 TYR cc_start: 0.8881 (m-80) cc_final: 0.8662 (m-80) REVERT: B 55 ASP cc_start: 0.8366 (t0) cc_final: 0.8016 (t0) outliers start: 21 outliers final: 14 residues processed: 95 average time/residue: 0.1651 time to fit residues: 19.6119 Evaluate side-chains 91 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 148 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3971 Z= 0.247 Angle : 0.592 7.892 5391 Z= 0.305 Chirality : 0.043 0.124 628 Planarity : 0.004 0.049 663 Dihedral : 4.181 33.027 519 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.29 % Allowed : 25.17 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.38), residues: 488 helix: 1.42 (0.31), residues: 285 sheet: 0.72 (0.55), residues: 71 loop : 0.13 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 251 HIS 0.005 0.001 HIS A 334 PHE 0.008 0.001 PHE A 365 TYR 0.015 0.001 TYR B 37 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6419 (mt) REVERT: A 349 MET cc_start: 0.6771 (tpt) cc_final: 0.6128 (mtp) REVERT: B 37 TYR cc_start: 0.8902 (m-80) cc_final: 0.8638 (m-80) REVERT: B 55 ASP cc_start: 0.8407 (t0) cc_final: 0.7999 (t0) outliers start: 27 outliers final: 20 residues processed: 97 average time/residue: 0.1529 time to fit residues: 19.0369 Evaluate side-chains 96 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.0770 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 148 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3971 Z= 0.200 Angle : 0.603 10.500 5391 Z= 0.297 Chirality : 0.042 0.121 628 Planarity : 0.004 0.049 663 Dihedral : 4.079 32.698 519 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.53 % Allowed : 25.17 % Favored : 68.30 % 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: 1.35 (0.38), residues: 488 helix: 1.48 (0.31), residues: 286 sheet: 0.88 (0.56), residues: 69 loop : -0.26 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 251 HIS 0.004 0.001 HIS A 334 PHE 0.010 0.001 PHE A 82 TYR 0.014 0.001 TYR B 98 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6343 (mt) REVERT: A 349 MET cc_start: 0.6726 (tpt) cc_final: 0.6109 (mtp) REVERT: A 389 MET cc_start: 0.9004 (ttp) cc_final: 0.8773 (ttt) REVERT: B 37 TYR cc_start: 0.8889 (m-80) cc_final: 0.8623 (m-80) REVERT: B 55 ASP cc_start: 0.8395 (t0) cc_final: 0.7965 (t0) outliers start: 28 outliers final: 20 residues processed: 99 average time/residue: 0.1231 time to fit residues: 15.7401 Evaluate side-chains 104 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 148 ASN A 209 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3971 Z= 0.226 Angle : 0.592 8.528 5391 Z= 0.297 Chirality : 0.042 0.122 628 Planarity : 0.004 0.048 663 Dihedral : 4.119 33.438 519 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.29 % Allowed : 25.17 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.38), residues: 488 helix: 1.47 (0.31), residues: 286 sheet: 0.83 (0.56), residues: 71 loop : -0.24 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 251 HIS 0.003 0.001 HIS A 334 PHE 0.007 0.001 PHE A 365 TYR 0.014 0.001 TYR A 119 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6372 (mt) REVERT: A 349 MET cc_start: 0.6743 (tpt) cc_final: 0.6125 (mtp) REVERT: B 3 GLN cc_start: 0.7634 (mp10) cc_final: 0.7288 (pm20) REVERT: B 37 TYR cc_start: 0.8892 (m-80) cc_final: 0.8607 (m-80) REVERT: B 55 ASP cc_start: 0.8442 (t0) cc_final: 0.8005 (t0) REVERT: B 118 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7669 (tp-100) outliers start: 27 outliers final: 21 residues processed: 99 average time/residue: 0.1333 time to fit residues: 16.9412 Evaluate side-chains 102 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.0670 chunk 28 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.0010 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 209 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3971 Z= 0.166 Angle : 0.594 8.036 5391 Z= 0.297 Chirality : 0.041 0.120 628 Planarity : 0.004 0.048 663 Dihedral : 4.028 32.985 519 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.43 % Allowed : 27.74 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.38), residues: 488 helix: 1.50 (0.31), residues: 287 sheet: 0.99 (0.56), residues: 69 loop : -0.39 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.008 0.001 HIS A 334 PHE 0.013 0.001 PHE A 116 TYR 0.013 0.001 TYR B 98 ARG 0.001 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6302 (mt) REVERT: A 349 MET cc_start: 0.6680 (tpt) cc_final: 0.6081 (mtp) REVERT: A 403 TYR cc_start: 0.9022 (m-80) cc_final: 0.8745 (m-10) REVERT: B 3 GLN cc_start: 0.7651 (mp10) cc_final: 0.7315 (pm20) REVERT: B 37 TYR cc_start: 0.8844 (m-80) cc_final: 0.8567 (m-80) REVERT: B 55 ASP cc_start: 0.8428 (t0) cc_final: 0.7986 (t0) REVERT: B 105 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.5023 (p90) REVERT: B 118 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7485 (tp-100) outliers start: 19 outliers final: 14 residues processed: 90 average time/residue: 0.1406 time to fit residues: 16.2682 Evaluate side-chains 98 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 105 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3971 Z= 0.198 Angle : 0.596 8.030 5391 Z= 0.299 Chirality : 0.042 0.124 628 Planarity : 0.004 0.048 663 Dihedral : 4.032 33.000 519 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.43 % Allowed : 27.97 % Favored : 67.60 % 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: 1.34 (0.38), residues: 488 helix: 1.53 (0.31), residues: 285 sheet: 0.83 (0.56), residues: 71 loop : -0.38 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.006 0.001 HIS A 334 PHE 0.010 0.001 PHE A 116 TYR 0.015 0.001 TYR A 240 ARG 0.001 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8031 (tpp) cc_final: 0.7744 (tpp) REVERT: A 93 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6334 (mt) REVERT: A 349 MET cc_start: 0.6714 (tpt) cc_final: 0.6097 (mtp) REVERT: B 3 GLN cc_start: 0.7658 (mp10) cc_final: 0.7311 (pm20) REVERT: B 37 TYR cc_start: 0.8841 (m-80) cc_final: 0.8551 (m-80) REVERT: B 55 ASP cc_start: 0.8471 (t0) cc_final: 0.8009 (t0) REVERT: B 105 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.4867 (p90) REVERT: B 118 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7457 (tp-100) outliers start: 19 outliers final: 13 residues processed: 90 average time/residue: 0.1343 time to fit residues: 15.5814 Evaluate side-chains 95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 105 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.0980 chunk 41 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 148 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3971 Z= 0.176 Angle : 0.594 7.958 5391 Z= 0.296 Chirality : 0.041 0.123 628 Planarity : 0.004 0.048 663 Dihedral : 4.002 32.696 519 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.96 % Allowed : 29.14 % Favored : 66.90 % 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: 1.41 (0.39), residues: 488 helix: 1.56 (0.31), residues: 287 sheet: 1.01 (0.57), residues: 69 loop : -0.41 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.006 0.001 HIS A 334 PHE 0.008 0.001 PHE A 82 TYR 0.013 0.001 TYR B 98 ARG 0.001 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6260 (mt) REVERT: A 153 MET cc_start: 0.7951 (tpt) cc_final: 0.7474 (ttt) REVERT: A 349 MET cc_start: 0.6681 (tpt) cc_final: 0.6074 (mtp) REVERT: A 403 TYR cc_start: 0.9023 (m-80) cc_final: 0.8755 (m-10) REVERT: B 3 GLN cc_start: 0.7651 (mp10) cc_final: 0.7313 (pm20) REVERT: B 37 TYR cc_start: 0.8828 (m-80) cc_final: 0.8549 (m-80) REVERT: B 55 ASP cc_start: 0.8471 (t0) cc_final: 0.8013 (t0) REVERT: B 105 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.4777 (p90) REVERT: B 118 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7438 (tp-100) outliers start: 17 outliers final: 14 residues processed: 91 average time/residue: 0.1261 time to fit residues: 15.1318 Evaluate side-chains 95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 105 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 5 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.0040 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3971 Z= 0.175 Angle : 0.590 8.011 5391 Z= 0.296 Chirality : 0.041 0.124 628 Planarity : 0.004 0.048 663 Dihedral : 3.971 32.805 519 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.50 % Allowed : 30.07 % Favored : 66.43 % 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: 1.36 (0.39), residues: 488 helix: 1.55 (0.31), residues: 287 sheet: 0.79 (0.56), residues: 71 loop : -0.38 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 251 HIS 0.005 0.001 HIS A 334 PHE 0.007 0.001 PHE A 42 TYR 0.016 0.001 TYR A 240 ARG 0.001 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8296 (mmm) cc_final: 0.8006 (mmm) REVERT: A 153 MET cc_start: 0.7970 (tpt) cc_final: 0.7518 (ttt) REVERT: A 173 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: A 349 MET cc_start: 0.6680 (tpt) cc_final: 0.6075 (mtp) REVERT: A 403 TYR cc_start: 0.9005 (m-80) cc_final: 0.8742 (m-10) REVERT: B 3 GLN cc_start: 0.7636 (mp10) cc_final: 0.7291 (pm20) REVERT: B 37 TYR cc_start: 0.8814 (m-80) cc_final: 0.8543 (m-80) REVERT: B 55 ASP cc_start: 0.8468 (t0) cc_final: 0.8015 (t0) REVERT: B 105 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.4604 (p90) REVERT: B 118 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7429 (tp-100) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.1254 time to fit residues: 15.2520 Evaluate side-chains 95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 105 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102294 restraints weight = 5426.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105332 restraints weight = 3167.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107136 restraints weight = 2265.794| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3971 Z= 0.202 Angle : 0.600 8.047 5391 Z= 0.302 Chirality : 0.042 0.127 628 Planarity : 0.004 0.048 663 Dihedral : 3.985 32.480 519 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.96 % Allowed : 29.60 % Favored : 66.43 % 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: 1.32 (0.39), residues: 488 helix: 1.54 (0.31), residues: 285 sheet: 0.90 (0.57), residues: 69 loop : -0.49 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 251 HIS 0.005 0.001 HIS A 334 PHE 0.008 0.001 PHE A 42 TYR 0.014 0.001 TYR B 98 ARG 0.001 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.44 seconds wall clock time: 24 minutes 30.63 seconds (1470.63 seconds total)