Starting phenix.real_space_refine on Wed Jun 4 15:20:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uwd_64550/06_2025/9uwd_64550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uwd_64550/06_2025/9uwd_64550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uwd_64550/06_2025/9uwd_64550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uwd_64550/06_2025/9uwd_64550.map" model { file = "/net/cci-nas-00/data/ceres_data/9uwd_64550/06_2025/9uwd_64550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uwd_64550/06_2025/9uwd_64550.cif" } resolution = 3.41 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= -0.000 sd= 0.063 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 24 5.16 5 C 2176 2.51 5 N 565 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3355 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3355 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 410} Time building chain proxies: 3.62, per 1000 atoms: 1.08 Number of scatterers: 3355 At special positions: 0 Unit cell: (59.13, 87.6, 110.96, 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 24 16.00 O 590 8.00 N 565 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 178 " distance=1.95 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 183 " 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: 0.86 Conformation dependent library (CDL) restraints added in 412.6 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 810 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 1 sheets defined 79.9% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 45 removed outlier: 3.640A pdb=" N GLY A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 90 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 92 through 97 removed outlier: 4.231A pdb=" N ALA A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 134 removed outlier: 3.824A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 147 through 164 removed outlier: 4.861A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 193 through 250 removed outlier: 3.885A pdb=" N TYR A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 274 removed outlier: 3.966A pdb=" N LYS A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 313 removed outlier: 3.675A pdb=" N PHE A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 378 removed outlier: 3.914A pdb=" N ASN A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.577A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 415 removed outlier: 3.749A pdb=" N ILE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Proline residue: A 408 - end of helix removed outlier: 4.407A pdb=" N ILE A 413 " --> pdb=" O TRP A 409 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.660A pdb=" N ARG A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 176 256 hydrogen bonds defined for protein. 768 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: 0.97 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 538 1.31 - 1.43: 895 1.43 - 1.56: 1956 1.56 - 1.68: 1 1.68 - 1.81: 37 Bond restraints: 3427 Sorted by residual: bond pdb=" N THR A 181 " pdb=" CA THR A 181 " ideal model delta sigma weight residual 1.463 1.379 0.084 1.08e-02 8.57e+03 5.99e+01 bond pdb=" CA PRO A 408 " pdb=" C PRO A 408 " ideal model delta sigma weight residual 1.517 1.440 0.077 1.46e-02 4.69e+03 2.76e+01 bond pdb=" C ILE A 403 " pdb=" O ILE A 403 " ideal model delta sigma weight residual 1.237 1.182 0.056 1.17e-02 7.31e+03 2.26e+01 bond pdb=" N ILE A 405 " pdb=" CA ILE A 405 " ideal model delta sigma weight residual 1.461 1.408 0.053 1.17e-02 7.31e+03 2.09e+01 bond pdb=" CA TRP A 182 " pdb=" C TRP A 182 " ideal model delta sigma weight residual 1.524 1.467 0.056 1.26e-02 6.30e+03 1.99e+01 ... (remaining 3422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 4554 3.22 - 6.44: 62 6.44 - 9.67: 18 9.67 - 12.89: 6 12.89 - 16.11: 1 Bond angle restraints: 4641 Sorted by residual: angle pdb=" C ASP A 407 " pdb=" N PRO A 408 " pdb=" CA PRO A 408 " ideal model delta sigma weight residual 119.05 102.94 16.11 1.11e+00 8.12e-01 2.11e+02 angle pdb=" CA PRO A 408 " pdb=" N PRO A 408 " pdb=" CD PRO A 408 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 angle pdb=" C ILE A 410 " pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 112.04 102.34 9.70 1.31e+00 5.83e-01 5.48e+01 angle pdb=" N THR A 181 " pdb=" CA THR A 181 " pdb=" C THR A 181 " ideal model delta sigma weight residual 111.04 99.82 11.22 1.55e+00 4.16e-01 5.24e+01 angle pdb=" N TRP A 182 " pdb=" CA TRP A 182 " pdb=" C TRP A 182 " ideal model delta sigma weight residual 110.23 119.41 -9.18 1.45e+00 4.76e-01 4.01e+01 ... (remaining 4636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1992 17.12 - 34.23: 55 34.23 - 51.35: 13 51.35 - 68.46: 4 68.46 - 85.58: 3 Dihedral angle restraints: 2067 sinusoidal: 817 harmonic: 1250 Sorted by residual: dihedral pdb=" C VAL A 406 " pdb=" N VAL A 406 " pdb=" CA VAL A 406 " pdb=" CB VAL A 406 " ideal model delta harmonic sigma weight residual -122.00 -146.07 24.07 0 2.50e+00 1.60e-01 9.27e+01 dihedral pdb=" CB CYS A 8 " pdb=" SG CYS A 8 " pdb=" SG CYS A 178 " pdb=" CB CYS A 178 " ideal model delta sinusoidal sigma weight residual -86.00 -166.05 80.05 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" N VAL A 406 " pdb=" C VAL A 406 " pdb=" CA VAL A 406 " pdb=" CB VAL A 406 " ideal model delta harmonic sigma weight residual 123.40 144.50 -21.10 0 2.50e+00 1.60e-01 7.12e+01 ... (remaining 2064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 518 0.183 - 0.366: 12 0.366 - 0.549: 3 0.549 - 0.732: 1 0.732 - 0.915: 1 Chirality restraints: 535 Sorted by residual: chirality pdb=" CA VAL A 406 " pdb=" N VAL A 406 " pdb=" C VAL A 406 " pdb=" CB VAL A 406 " both_signs ideal model delta sigma weight residual False 2.44 1.53 0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CA PHE A 427 " pdb=" N PHE A 427 " pdb=" C PHE A 427 " pdb=" CB PHE A 427 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.83e+00 chirality pdb=" CA TRP A 409 " pdb=" N TRP A 409 " pdb=" C TRP A 409 " pdb=" CB TRP A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 532 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 407 " 0.128 5.00e-02 4.00e+02 1.83e-01 5.33e+01 pdb=" N PRO A 408 " -0.314 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.113 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 421 " 0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ILE A 421 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE A 421 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A 422 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 374 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C TYR A 374 " -0.041 2.00e-02 2.50e+03 pdb=" O TYR A 374 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 375 " 0.014 2.00e-02 2.50e+03 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 29 2.58 - 3.16: 2928 3.16 - 3.74: 5198 3.74 - 4.32: 6632 4.32 - 4.90: 11352 Nonbonded interactions: 26139 Sorted by model distance: nonbonded pdb=" CD2 LEU A 345 " pdb=" CZ PHE A 427 " model vdw 2.001 3.760 nonbonded pdb=" O LYS A 327 " pdb=" ND2 ASN A 331 " model vdw 2.203 3.120 nonbonded pdb=" O GLY A 45 " pdb=" NH2 ARG A 55 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASN A 385 " pdb=" N SER A 388 " model vdw 2.240 3.120 nonbonded pdb=" CG ARG A 229 " pdb=" CE1 PHE A 427 " model vdw 2.248 3.740 ... (remaining 26134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 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 : 0.007 0.084 3429 Z= 0.513 Angle : 1.072 25.378 4645 Z= 0.689 Chirality : 0.077 0.915 535 Planarity : 0.009 0.183 584 Dihedral : 9.295 85.581 1251 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.52 % Favored : 96.01 % Rotamer: Outliers : 1.39 % Allowed : 4.17 % Favored : 94.44 % Cbeta Deviations : 0.74 % 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: 1.54 (0.41), residues: 426 helix: 2.42 (0.28), residues: 303 sheet: None (None), residues: 0 loop : -2.83 (0.48), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 182 HIS 0.002 0.000 HIS A 424 PHE 0.016 0.001 PHE A 174 TYR 0.029 0.001 TYR A 375 ARG 0.002 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.11698 ( 256) hydrogen bonds : angle 4.29628 ( 768) SS BOND : bond 0.05818 ( 2) SS BOND : angle 14.67466 ( 4) covalent geometry : bond 0.00695 ( 3427) covalent geometry : angle 0.98185 ( 4641) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.448 Fit side-chains REVERT: A 181 THR cc_start: 0.7674 (p) cc_final: 0.7395 (p) REVERT: A 375 TYR cc_start: 0.5361 (OUTLIER) cc_final: 0.4859 (t80) outliers start: 5 outliers final: 1 residues processed: 101 average time/residue: 0.1745 time to fit residues: 20.8915 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN A 238 ASN A 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.231500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.198672 restraints weight = 4486.072| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.84 r_work: 0.4055 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3429 Z= 0.137 Angle : 0.643 6.993 4645 Z= 0.315 Chirality : 0.038 0.155 535 Planarity : 0.005 0.067 584 Dihedral : 4.505 51.239 468 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.61 % Allowed : 12.78 % Favored : 83.61 % 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: 2.57 (0.43), residues: 426 helix: 2.68 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.79 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 409 HIS 0.009 0.001 HIS A 136 PHE 0.017 0.002 PHE A 414 TYR 0.027 0.002 TYR A 87 ARG 0.003 0.001 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 256) hydrogen bonds : angle 3.65696 ( 768) SS BOND : bond 0.00588 ( 2) SS BOND : angle 3.42725 ( 4) covalent geometry : bond 0.00306 ( 3427) covalent geometry : angle 0.63535 ( 4641) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.370 Fit side-chains REVERT: A 63 MET cc_start: 0.7354 (ttm) cc_final: 0.7125 (ttm) REVERT: A 147 ARG cc_start: 0.6464 (mpp-170) cc_final: 0.5872 (ttp-170) REVERT: A 169 MET cc_start: 0.4836 (mtt) cc_final: 0.4033 (mtp) REVERT: A 265 MET cc_start: 0.7775 (ttp) cc_final: 0.7416 (mmm) REVERT: A 375 TYR cc_start: 0.5253 (OUTLIER) cc_final: 0.4681 (t80) outliers start: 13 outliers final: 7 residues processed: 72 average time/residue: 0.1974 time to fit residues: 16.7568 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 375 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN ** A 424 HIS ** 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 = 0.4419 r_free = 0.4419 target = 0.212385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175998 restraints weight = 4537.242| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.85 r_work: 0.3978 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3429 Z= 0.174 Angle : 0.698 7.580 4645 Z= 0.344 Chirality : 0.041 0.206 535 Planarity : 0.005 0.045 584 Dihedral : 4.774 49.763 467 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.28 % Allowed : 11.94 % Favored : 82.78 % 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: 2.26 (0.43), residues: 426 helix: 2.51 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -1.79 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 131 HIS 0.006 0.002 HIS A 136 PHE 0.017 0.002 PHE A 414 TYR 0.042 0.003 TYR A 87 ARG 0.004 0.001 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 256) hydrogen bonds : angle 4.03996 ( 768) SS BOND : bond 0.00641 ( 2) SS BOND : angle 2.34362 ( 4) covalent geometry : bond 0.00392 ( 3427) covalent geometry : angle 0.69489 ( 4641) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.408 Fit side-chains REVERT: A 63 MET cc_start: 0.7600 (ttm) cc_final: 0.7318 (ttm) REVERT: A 147 ARG cc_start: 0.6977 (mpp-170) cc_final: 0.5575 (ttp-170) REVERT: A 169 MET cc_start: 0.5894 (mtt) cc_final: 0.5066 (mtp) REVERT: A 361 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7181 (tp) REVERT: A 375 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5083 (t80) outliers start: 19 outliers final: 11 residues processed: 78 average time/residue: 0.1615 time to fit residues: 15.6654 Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 422 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.211007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174657 restraints weight = 4725.083| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.77 r_work: 0.3843 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3429 Z= 0.186 Angle : 0.729 11.620 4645 Z= 0.356 Chirality : 0.041 0.201 535 Planarity : 0.005 0.040 584 Dihedral : 4.858 47.798 467 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.83 % Allowed : 13.06 % Favored : 81.11 % 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: 1.94 (0.43), residues: 426 helix: 2.33 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -2.08 (0.59), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 131 HIS 0.004 0.001 HIS A 136 PHE 0.018 0.002 PHE A 114 TYR 0.033 0.002 TYR A 87 ARG 0.003 0.001 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 256) hydrogen bonds : angle 4.09120 ( 768) SS BOND : bond 0.00360 ( 2) SS BOND : angle 2.26213 ( 4) covalent geometry : bond 0.00429 ( 3427) covalent geometry : angle 0.72596 ( 4641) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 13 SER cc_start: 0.8659 (m) cc_final: 0.8157 (p) REVERT: A 63 MET cc_start: 0.7560 (ttm) cc_final: 0.6781 (mmt) REVERT: A 147 ARG cc_start: 0.7250 (mpp-170) cc_final: 0.5332 (ttp-170) REVERT: A 169 MET cc_start: 0.6257 (mtt) cc_final: 0.5172 (mtp) REVERT: A 186 GLN cc_start: 0.6161 (tt0) cc_final: 0.5590 (tp40) REVERT: A 187 MET cc_start: 0.7302 (mtm) cc_final: 0.6957 (mtp) REVERT: A 205 SER cc_start: 0.7438 (t) cc_final: 0.7128 (p) REVERT: A 375 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.4925 (t80) outliers start: 21 outliers final: 15 residues processed: 80 average time/residue: 0.1652 time to fit residues: 16.3268 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 7 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 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN A 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.206102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.168775 restraints weight = 4764.030| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.89 r_work: 0.3865 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3429 Z= 0.132 Angle : 0.633 9.954 4645 Z= 0.307 Chirality : 0.038 0.180 535 Planarity : 0.004 0.039 584 Dihedral : 4.568 46.540 467 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.72 % Allowed : 15.56 % Favored : 79.72 % 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: 2.35 (0.43), residues: 426 helix: 2.63 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.98 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 409 HIS 0.002 0.001 HIS A 136 PHE 0.016 0.002 PHE A 114 TYR 0.026 0.002 TYR A 87 ARG 0.003 0.000 ARG A 420 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 256) hydrogen bonds : angle 3.82864 ( 768) SS BOND : bond 0.00127 ( 2) SS BOND : angle 1.91675 ( 4) covalent geometry : bond 0.00304 ( 3427) covalent geometry : angle 0.63032 ( 4641) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8473 (m) cc_final: 0.8053 (p) REVERT: A 63 MET cc_start: 0.7599 (ttm) cc_final: 0.7328 (ttm) REVERT: A 147 ARG cc_start: 0.7336 (mpp-170) cc_final: 0.5321 (ttp-170) REVERT: A 169 MET cc_start: 0.6176 (mtt) cc_final: 0.5159 (mtp) REVERT: A 205 SER cc_start: 0.7262 (t) cc_final: 0.7020 (p) REVERT: A 361 LEU cc_start: 0.7757 (tt) cc_final: 0.7071 (mm) REVERT: A 375 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4788 (t80) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.1462 time to fit residues: 14.0299 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 422 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.0070 chunk 40 optimal weight: 0.2980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.209381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.171941 restraints weight = 4806.677| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.95 r_work: 0.3901 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3429 Z= 0.112 Angle : 0.602 9.308 4645 Z= 0.293 Chirality : 0.036 0.165 535 Planarity : 0.004 0.038 584 Dihedral : 4.334 45.865 467 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.61 % Allowed : 17.50 % Favored : 78.89 % 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: 2.64 (0.43), residues: 426 helix: 2.92 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.98 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 239 HIS 0.002 0.000 HIS A 136 PHE 0.018 0.002 PHE A 5 TYR 0.022 0.001 TYR A 87 ARG 0.001 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 256) hydrogen bonds : angle 3.64391 ( 768) SS BOND : bond 0.00288 ( 2) SS BOND : angle 1.11882 ( 4) covalent geometry : bond 0.00251 ( 3427) covalent geometry : angle 0.60163 ( 4641) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8263 (m) cc_final: 0.7926 (p) REVERT: A 43 ARG cc_start: 0.6461 (mtt-85) cc_final: 0.5959 (tpt90) REVERT: A 63 MET cc_start: 0.7544 (ttm) cc_final: 0.7280 (ttm) REVERT: A 147 ARG cc_start: 0.7324 (mpp-170) cc_final: 0.5280 (ttp-170) REVERT: A 169 MET cc_start: 0.6078 (mtt) cc_final: 0.5063 (mtp) REVERT: A 205 SER cc_start: 0.7105 (t) cc_final: 0.6895 (p) REVERT: A 207 MET cc_start: 0.7826 (ttt) cc_final: 0.7540 (ttt) REVERT: A 238 ASN cc_start: 0.8548 (m110) cc_final: 0.8190 (m-40) REVERT: A 375 TYR cc_start: 0.5257 (OUTLIER) cc_final: 0.4621 (t80) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.1617 time to fit residues: 14.5592 Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 422 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.215607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.179748 restraints weight = 4681.411| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.77 r_work: 0.3886 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3429 Z= 0.130 Angle : 0.635 8.564 4645 Z= 0.306 Chirality : 0.037 0.156 535 Planarity : 0.004 0.040 584 Dihedral : 4.427 46.123 467 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.56 % Allowed : 16.67 % Favored : 77.78 % 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: 2.62 (0.43), residues: 426 helix: 2.92 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -1.97 (0.57), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 239 HIS 0.002 0.001 HIS A 136 PHE 0.016 0.002 PHE A 114 TYR 0.033 0.002 TYR A 87 ARG 0.002 0.000 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 256) hydrogen bonds : angle 3.72994 ( 768) SS BOND : bond 0.00163 ( 2) SS BOND : angle 1.59603 ( 4) covalent geometry : bond 0.00302 ( 3427) covalent geometry : angle 0.63334 ( 4641) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8238 (m) cc_final: 0.7696 (p) REVERT: A 43 ARG cc_start: 0.6592 (mtt-85) cc_final: 0.6076 (tpt90) REVERT: A 63 MET cc_start: 0.7638 (ttm) cc_final: 0.7421 (ttm) REVERT: A 169 MET cc_start: 0.6327 (mtt) cc_final: 0.5341 (mtp) REVERT: A 186 GLN cc_start: 0.5927 (tt0) cc_final: 0.5524 (tp40) REVERT: A 205 SER cc_start: 0.7294 (t) cc_final: 0.7048 (p) REVERT: A 361 LEU cc_start: 0.7774 (tt) cc_final: 0.7074 (mm) REVERT: A 371 TYR cc_start: 0.5785 (t80) cc_final: 0.4662 (m-80) REVERT: A 375 TYR cc_start: 0.5620 (OUTLIER) cc_final: 0.5210 (m-80) outliers start: 20 outliers final: 16 residues processed: 78 average time/residue: 0.1299 time to fit residues: 12.8119 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 422 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 39 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: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.214968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.178537 restraints weight = 4804.593| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.90 r_work: 0.3920 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3429 Z= 0.126 Angle : 0.619 8.139 4645 Z= 0.304 Chirality : 0.036 0.155 535 Planarity : 0.004 0.038 584 Dihedral : 4.428 46.485 467 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.28 % Allowed : 17.22 % Favored : 77.50 % 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: 2.47 (0.43), residues: 426 helix: 2.82 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -2.19 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 409 HIS 0.008 0.001 HIS A 424 PHE 0.016 0.002 PHE A 414 TYR 0.031 0.002 TYR A 87 ARG 0.002 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 256) hydrogen bonds : angle 3.76571 ( 768) SS BOND : bond 0.00151 ( 2) SS BOND : angle 1.44215 ( 4) covalent geometry : bond 0.00292 ( 3427) covalent geometry : angle 0.61789 ( 4641) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8187 (m) cc_final: 0.7681 (p) REVERT: A 43 ARG cc_start: 0.6632 (mtt-85) cc_final: 0.6094 (tpt90) REVERT: A 63 MET cc_start: 0.7679 (ttm) cc_final: 0.7470 (ttm) REVERT: A 169 MET cc_start: 0.6313 (mtt) cc_final: 0.5331 (mtp) REVERT: A 186 GLN cc_start: 0.5926 (tt0) cc_final: 0.5541 (tp40) REVERT: A 205 SER cc_start: 0.7186 (t) cc_final: 0.6971 (p) REVERT: A 361 LEU cc_start: 0.7776 (tt) cc_final: 0.7063 (mm) REVERT: A 371 TYR cc_start: 0.5789 (t80) cc_final: 0.4652 (m-80) REVERT: A 375 TYR cc_start: 0.5590 (OUTLIER) cc_final: 0.5202 (m-80) REVERT: A 424 HIS cc_start: 0.5858 (t70) cc_final: 0.5583 (t-90) outliers start: 19 outliers final: 18 residues processed: 76 average time/residue: 0.1331 time to fit residues: 12.7999 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 422 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.214675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178168 restraints weight = 4702.702| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.86 r_work: 0.3899 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3429 Z= 0.117 Angle : 0.600 7.645 4645 Z= 0.294 Chirality : 0.036 0.153 535 Planarity : 0.004 0.037 584 Dihedral : 4.375 47.976 467 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.72 % Allowed : 17.78 % Favored : 77.50 % 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: 2.55 (0.43), residues: 426 helix: 2.87 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -2.11 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 239 HIS 0.005 0.001 HIS A 424 PHE 0.016 0.002 PHE A 414 TYR 0.031 0.002 TYR A 87 ARG 0.002 0.000 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 256) hydrogen bonds : angle 3.69904 ( 768) SS BOND : bond 0.00082 ( 2) SS BOND : angle 1.14122 ( 4) covalent geometry : bond 0.00266 ( 3427) covalent geometry : angle 0.59961 ( 4641) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 13 SER cc_start: 0.8029 (m) cc_final: 0.7529 (p) REVERT: A 43 ARG cc_start: 0.6687 (mtt-85) cc_final: 0.6028 (tpt90) REVERT: A 63 MET cc_start: 0.7671 (ttm) cc_final: 0.7446 (ttm) REVERT: A 169 MET cc_start: 0.6293 (mtt) cc_final: 0.5319 (mtp) REVERT: A 361 LEU cc_start: 0.7714 (tt) cc_final: 0.6996 (mm) REVERT: A 371 TYR cc_start: 0.5717 (t80) cc_final: 0.4578 (m-80) REVERT: A 375 TYR cc_start: 0.5395 (OUTLIER) cc_final: 0.5060 (m-80) outliers start: 17 outliers final: 15 residues processed: 70 average time/residue: 0.1411 time to fit residues: 12.5304 Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 422 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.0030 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.211243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.174752 restraints weight = 4654.056| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.86 r_work: 0.3878 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3429 Z= 0.128 Angle : 0.631 8.590 4645 Z= 0.311 Chirality : 0.036 0.153 535 Planarity : 0.004 0.038 584 Dihedral : 4.436 48.783 467 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.00 % Allowed : 17.22 % Favored : 77.78 % 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: 2.52 (0.43), residues: 426 helix: 2.84 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.13 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 239 HIS 0.002 0.001 HIS A 424 PHE 0.015 0.002 PHE A 114 TYR 0.030 0.002 TYR A 87 ARG 0.002 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 256) hydrogen bonds : angle 3.72645 ( 768) SS BOND : bond 0.00132 ( 2) SS BOND : angle 1.23468 ( 4) covalent geometry : bond 0.00297 ( 3427) covalent geometry : angle 0.63016 ( 4641) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8042 (m) cc_final: 0.7550 (p) REVERT: A 43 ARG cc_start: 0.6743 (mtt-85) cc_final: 0.6096 (tpt90) REVERT: A 63 MET cc_start: 0.7655 (ttm) cc_final: 0.7414 (ttm) REVERT: A 169 MET cc_start: 0.6417 (mtt) cc_final: 0.5308 (mtp) REVERT: A 222 MET cc_start: 0.7168 (mmm) cc_final: 0.6917 (tpp) REVERT: A 361 LEU cc_start: 0.7726 (tt) cc_final: 0.7000 (mm) REVERT: A 371 TYR cc_start: 0.5685 (t80) cc_final: 0.4584 (m-80) REVERT: A 375 TYR cc_start: 0.5507 (OUTLIER) cc_final: 0.5162 (m-80) outliers start: 18 outliers final: 17 residues processed: 68 average time/residue: 0.1343 time to fit residues: 11.6548 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 422 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.205892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169262 restraints weight = 4680.629| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.86 r_work: 0.3874 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3429 Z= 0.131 Angle : 0.632 8.347 4645 Z= 0.310 Chirality : 0.037 0.155 535 Planarity : 0.004 0.038 584 Dihedral : 4.508 49.519 467 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.83 % Allowed : 16.67 % Favored : 77.50 % 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: 2.55 (0.43), residues: 426 helix: 2.85 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.08 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 239 HIS 0.002 0.001 HIS A 136 PHE 0.015 0.002 PHE A 414 TYR 0.026 0.002 TYR A 87 ARG 0.002 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 256) hydrogen bonds : angle 3.73621 ( 768) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.24755 ( 4) covalent geometry : bond 0.00302 ( 3427) covalent geometry : angle 0.63157 ( 4641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1969.98 seconds wall clock time: 34 minutes 40.48 seconds (2080.48 seconds total)