Starting phenix.real_space_refine on Wed Sep 17 03:41:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uwd_64550/09_2025/9uwd_64550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uwd_64550/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9uwd_64550/09_2025/9uwd_64550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uwd_64550/09_2025/9uwd_64550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uwd_64550/09_2025/9uwd_64550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uwd_64550/09_2025/9uwd_64550.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.94, per 1000 atoms: 0.28 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: 0.29 Conformation dependent library (CDL) restraints added in 131.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.08 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: 0.42 Time building geometry restraints manager: 0.39 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.740 Find NCS groups from input model: 0.010 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.320 ------------------------------------------------------------------------------- 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 : 10.74 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG A 142 TYR 0.029 0.001 TYR A 375 PHE 0.016 0.001 PHE A 174 TRP 0.013 0.001 TRP A 182 HIS 0.002 0.000 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 3427) covalent geometry : angle 0.98185 ( 4641) SS BOND : bond 0.05818 ( 2) SS BOND : angle 14.67466 ( 4) hydrogen bonds : bond 0.11698 ( 256) hydrogen bonds : angle 4.29628 ( 768) *********************** 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 : 0.102 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: 0.0782 time to fit residues: 9.3321 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 : 0.118 ------------------------------------------------------------------------------- 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 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.230726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.197673 restraints weight = 4540.910| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.84 r_work: 0.4052 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3429 Z= 0.145 Angle : 0.652 7.177 4645 Z= 0.319 Chirality : 0.039 0.165 535 Planarity : 0.005 0.068 584 Dihedral : 4.542 50.776 468 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.61 % Allowed : 12.50 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.43), residues: 426 helix: 2.66 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.77 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 266 TYR 0.028 0.002 TYR A 87 PHE 0.017 0.002 PHE A 414 TRP 0.010 0.002 TRP A 409 HIS 0.009 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3427) covalent geometry : angle 0.64471 ( 4641) SS BOND : bond 0.00657 ( 2) SS BOND : angle 3.37987 ( 4) hydrogen bonds : bond 0.03285 ( 256) hydrogen bonds : angle 3.68609 ( 768) *********************** 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 : 0.127 Fit side-chains REVERT: A 63 MET cc_start: 0.7365 (ttm) cc_final: 0.7119 (ttm) REVERT: A 147 ARG cc_start: 0.6480 (mpp-170) cc_final: 0.5897 (ttp-170) REVERT: A 169 MET cc_start: 0.4943 (mtt) cc_final: 0.4027 (mtp) REVERT: A 265 MET cc_start: 0.7785 (ttp) cc_final: 0.7447 (mmm) REVERT: A 375 TYR cc_start: 0.5232 (OUTLIER) cc_final: 0.4631 (t80) outliers start: 13 outliers final: 6 residues processed: 73 average time/residue: 0.0822 time to fit residues: 7.0641 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.091 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4429 r_free = 0.4429 target = 0.213584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.177125 restraints weight = 4569.708| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.89 r_work: 0.3985 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3429 Z= 0.161 Angle : 0.679 7.253 4645 Z= 0.334 Chirality : 0.041 0.179 535 Planarity : 0.005 0.045 584 Dihedral : 4.732 50.809 467 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.00 % Allowed : 11.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.43), residues: 426 helix: 2.52 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -1.66 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 43 TYR 0.040 0.003 TYR A 87 PHE 0.016 0.002 PHE A 414 TRP 0.010 0.002 TRP A 131 HIS 0.006 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3427) covalent geometry : angle 0.67589 ( 4641) SS BOND : bond 0.00574 ( 2) SS BOND : angle 2.31537 ( 4) hydrogen bonds : bond 0.03567 ( 256) hydrogen bonds : angle 3.96988 ( 768) *********************** 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 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.074 Fit side-chains REVERT: A 7 ARG cc_start: 0.6792 (ppt170) cc_final: 0.6579 (ppt170) REVERT: A 63 MET cc_start: 0.7606 (ttm) cc_final: 0.7325 (ttm) REVERT: A 147 ARG cc_start: 0.6973 (mpp-170) cc_final: 0.5655 (ttp-170) REVERT: A 169 MET cc_start: 0.5811 (mtt) cc_final: 0.4994 (mtp) REVERT: A 197 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6200 (mt) REVERT: A 361 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7171 (tp) REVERT: A 375 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.5051 (t80) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 0.0643 time to fit residues: 6.0364 Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 197 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 331 ASN 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 13 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.0060 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.219377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.182499 restraints weight = 4652.640| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.89 r_work: 0.3932 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3429 Z= 0.112 Angle : 0.608 10.250 4645 Z= 0.291 Chirality : 0.037 0.187 535 Planarity : 0.004 0.034 584 Dihedral : 4.460 49.878 467 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.17 % Allowed : 13.61 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.43), residues: 426 helix: 2.87 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.97 (0.58), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.032 0.002 TYR A 87 PHE 0.015 0.001 PHE A 414 TRP 0.009 0.001 TRP A 131 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3427) covalent geometry : angle 0.60608 ( 4641) SS BOND : bond 0.00524 ( 2) SS BOND : angle 1.73923 ( 4) hydrogen bonds : bond 0.02982 ( 256) hydrogen bonds : angle 3.67860 ( 768) *********************** 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 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.120 Fit side-chains REVERT: A 13 SER cc_start: 0.8467 (m) cc_final: 0.7919 (p) REVERT: A 43 ARG cc_start: 0.6040 (mtt-85) cc_final: 0.5643 (mtt-85) REVERT: A 63 MET cc_start: 0.7564 (ttm) cc_final: 0.7349 (ttm) REVERT: A 147 ARG cc_start: 0.6955 (mpp-170) cc_final: 0.5506 (ttp-170) REVERT: A 169 MET cc_start: 0.5776 (mtt) cc_final: 0.4782 (mtp) REVERT: A 197 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6063 (mt) REVERT: A 375 TYR cc_start: 0.5395 (OUTLIER) cc_final: 0.4596 (t80) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.0643 time to fit residues: 5.7944 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 197 LEU 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 339 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.0060 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4392 r_free = 0.4392 target = 0.209483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172830 restraints weight = 4635.221| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.81 r_work: 0.3909 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3429 Z= 0.114 Angle : 0.606 9.400 4645 Z= 0.290 Chirality : 0.036 0.159 535 Planarity : 0.004 0.037 584 Dihedral : 4.383 49.894 467 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.44 % Allowed : 13.33 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.43), residues: 426 helix: 2.92 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.96 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 266 TYR 0.025 0.002 TYR A 87 PHE 0.016 0.002 PHE A 5 TRP 0.007 0.001 TRP A 239 HIS 0.003 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3427) covalent geometry : angle 0.60458 ( 4641) SS BOND : bond 0.00147 ( 2) SS BOND : angle 1.37273 ( 4) hydrogen bonds : bond 0.02938 ( 256) hydrogen bonds : angle 3.64697 ( 768) *********************** 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 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 13 SER cc_start: 0.8267 (m) cc_final: 0.7785 (p) REVERT: A 43 ARG cc_start: 0.6300 (mtt-85) cc_final: 0.5947 (tpt90) REVERT: A 63 MET cc_start: 0.7600 (ttm) cc_final: 0.7146 (ttm) REVERT: A 147 ARG cc_start: 0.7022 (mpp-170) cc_final: 0.5342 (ttp-170) REVERT: A 169 MET cc_start: 0.5913 (mtt) cc_final: 0.4956 (mtp) REVERT: A 197 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.5972 (mt) REVERT: A 205 SER cc_start: 0.7052 (t) cc_final: 0.6834 (p) REVERT: A 207 MET cc_start: 0.7821 (ttt) cc_final: 0.7459 (ttt) REVERT: A 375 TYR cc_start: 0.5370 (OUTLIER) cc_final: 0.4609 (t80) outliers start: 16 outliers final: 11 residues processed: 72 average time/residue: 0.0673 time to fit residues: 5.9369 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 : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 339 GLU 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 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 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 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 = 0.4374 r_free = 0.4374 target = 0.207224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170046 restraints weight = 4739.543| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.77 r_work: 0.4000 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3429 Z= 0.129 Angle : 0.620 8.991 4645 Z= 0.300 Chirality : 0.037 0.144 535 Planarity : 0.004 0.039 584 Dihedral : 4.485 48.555 467 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.56 % Allowed : 13.61 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.43), residues: 426 helix: 2.93 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -2.23 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 55 TYR 0.022 0.002 TYR A 87 PHE 0.020 0.002 PHE A 5 TRP 0.008 0.001 TRP A 239 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3427) covalent geometry : angle 0.61913 ( 4641) SS BOND : bond 0.00228 ( 2) SS BOND : angle 1.30584 ( 4) hydrogen bonds : bond 0.03121 ( 256) hydrogen bonds : angle 3.73035 ( 768) *********************** 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 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8203 (m) cc_final: 0.7745 (p) REVERT: A 43 ARG cc_start: 0.6527 (mtt-85) cc_final: 0.6219 (tpt90) REVERT: A 147 ARG cc_start: 0.7274 (mpp-170) cc_final: 0.5408 (ttp-170) REVERT: A 169 MET cc_start: 0.6262 (mtt) cc_final: 0.5210 (mtp) REVERT: A 205 SER cc_start: 0.7183 (t) cc_final: 0.6973 (p) REVERT: A 238 ASN cc_start: 0.8622 (m110) cc_final: 0.8221 (m-40) REVERT: A 361 LEU cc_start: 0.7780 (tt) cc_final: 0.7155 (mm) REVERT: A 375 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.4834 (t80) outliers start: 20 outliers final: 16 residues processed: 83 average time/residue: 0.0630 time to fit residues: 6.4184 Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 105 CYS 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 331 ASN Chi-restraints excluded: chain A residue 339 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.209167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.173453 restraints weight = 4778.308| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.74 r_work: 0.3813 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3429 Z= 0.196 Angle : 0.736 9.583 4645 Z= 0.362 Chirality : 0.040 0.152 535 Planarity : 0.004 0.044 584 Dihedral : 4.900 48.170 467 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 7.22 % Allowed : 14.44 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.42), residues: 426 helix: 2.44 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -2.19 (0.56), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 266 TYR 0.013 0.002 TYR A 87 PHE 0.017 0.003 PHE A 414 TRP 0.011 0.002 TRP A 239 HIS 0.003 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 3427) covalent geometry : angle 0.73469 ( 4641) SS BOND : bond 0.00362 ( 2) SS BOND : angle 1.80423 ( 4) hydrogen bonds : bond 0.03806 ( 256) hydrogen bonds : angle 4.08474 ( 768) *********************** 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 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8418 (m) cc_final: 0.7979 (p) REVERT: A 63 MET cc_start: 0.7595 (ttm) cc_final: 0.6675 (mmt) REVERT: A 169 MET cc_start: 0.6572 (mtt) cc_final: 0.6113 (mtp) REVERT: A 186 GLN cc_start: 0.5979 (tt0) cc_final: 0.5552 (tp40) REVERT: A 205 SER cc_start: 0.7549 (t) cc_final: 0.7265 (p) REVERT: A 207 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7660 (ttt) REVERT: A 371 TYR cc_start: 0.5859 (t80) cc_final: 0.4413 (m-80) REVERT: A 375 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.4875 (t80) outliers start: 26 outliers final: 20 residues processed: 84 average time/residue: 0.0663 time to fit residues: 6.8912 Evaluate side-chains 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 71 THR 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 156 VAL Chi-restraints excluded: chain A residue 207 MET 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 339 GLU 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 Chi-restraints excluded: chain A residue 424 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 0.0370 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4449 r_free = 0.4449 target = 0.214181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178290 restraints weight = 4763.282| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.81 r_work: 0.3995 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3429 Z= 0.129 Angle : 0.658 9.595 4645 Z= 0.319 Chirality : 0.037 0.167 535 Planarity : 0.004 0.036 584 Dihedral : 4.571 48.393 467 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.39 % Allowed : 17.78 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.43), residues: 426 helix: 2.73 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -2.19 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 7 TYR 0.012 0.001 TYR A 87 PHE 0.017 0.002 PHE A 414 TRP 0.007 0.001 TRP A 48 HIS 0.003 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3427) covalent geometry : angle 0.65657 ( 4641) SS BOND : bond 0.00119 ( 2) SS BOND : angle 1.82904 ( 4) hydrogen bonds : bond 0.03180 ( 256) hydrogen bonds : angle 3.80664 ( 768) *********************** 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 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8269 (m) cc_final: 0.7986 (p) REVERT: A 43 ARG cc_start: 0.6548 (mtt-85) cc_final: 0.6074 (tpt90) REVERT: A 169 MET cc_start: 0.6454 (mtt) cc_final: 0.5967 (mtp) REVERT: A 185 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7378 (mt) REVERT: A 186 GLN cc_start: 0.5990 (tt0) cc_final: 0.5579 (tp40) REVERT: A 197 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.5923 (mt) REVERT: A 205 SER cc_start: 0.7226 (t) cc_final: 0.7017 (p) REVERT: A 207 MET cc_start: 0.7887 (ttt) cc_final: 0.7432 (ttt) REVERT: A 361 LEU cc_start: 0.7756 (tt) cc_final: 0.7101 (mm) REVERT: A 371 TYR cc_start: 0.5875 (t80) cc_final: 0.4687 (m-80) REVERT: A 375 TYR cc_start: 0.5608 (OUTLIER) cc_final: 0.5231 (m-80) outliers start: 23 outliers final: 19 residues processed: 78 average time/residue: 0.0537 time to fit residues: 5.3026 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 71 THR 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 156 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 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 339 GLU 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 Chi-restraints excluded: chain A residue 424 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4323 r_free = 0.4323 target = 0.201549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165385 restraints weight = 4838.171| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.77 r_work: 0.3847 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3429 Z= 0.172 Angle : 0.721 9.339 4645 Z= 0.351 Chirality : 0.039 0.159 535 Planarity : 0.004 0.040 584 Dihedral : 4.792 49.543 467 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.11 % Allowed : 18.61 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.42), residues: 426 helix: 2.50 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -2.18 (0.55), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 7 TYR 0.027 0.002 TYR A 87 PHE 0.016 0.002 PHE A 114 TRP 0.008 0.001 TRP A 239 HIS 0.002 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 3427) covalent geometry : angle 0.71843 ( 4641) SS BOND : bond 0.00311 ( 2) SS BOND : angle 2.24143 ( 4) hydrogen bonds : bond 0.03616 ( 256) hydrogen bonds : angle 3.92015 ( 768) *********************** 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 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8291 (m) cc_final: 0.8002 (p) REVERT: A 43 ARG cc_start: 0.6751 (mtt-85) cc_final: 0.6219 (tpt90) REVERT: A 169 MET cc_start: 0.6616 (mtt) cc_final: 0.6173 (mtp) REVERT: A 197 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6170 (mt) REVERT: A 205 SER cc_start: 0.7544 (t) cc_final: 0.7269 (p) REVERT: A 207 MET cc_start: 0.7894 (ttt) cc_final: 0.7546 (ttt) REVERT: A 236 GLU cc_start: 0.8344 (tp30) cc_final: 0.8070 (mm-30) REVERT: A 339 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: A 361 LEU cc_start: 0.7760 (tt) cc_final: 0.7048 (mm) REVERT: A 375 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.5293 (t80) outliers start: 22 outliers final: 17 residues processed: 75 average time/residue: 0.0650 time to fit residues: 6.0239 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 71 THR 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 156 VAL Chi-restraints excluded: chain A residue 197 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 339 GLU 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 Chi-restraints excluded: chain A residue 424 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4378 r_free = 0.4378 target = 0.207157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170333 restraints weight = 4722.076| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.87 r_work: 0.3873 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.6818 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 : 0.665 8.705 4645 Z= 0.324 Chirality : 0.037 0.162 535 Planarity : 0.004 0.036 584 Dihedral : 4.282 37.803 467 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.28 % Allowed : 19.44 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.42), residues: 426 helix: 2.70 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -2.35 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 94 TYR 0.024 0.002 TYR A 87 PHE 0.017 0.002 PHE A 414 TRP 0.006 0.001 TRP A 409 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3427) covalent geometry : angle 0.66341 ( 4641) SS BOND : bond 0.00153 ( 2) SS BOND : angle 1.49458 ( 4) hydrogen bonds : bond 0.03221 ( 256) hydrogen bonds : angle 3.78328 ( 768) ********************** 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 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 SER cc_start: 0.8212 (m) cc_final: 0.7772 (p) REVERT: A 43 ARG cc_start: 0.6661 (mtt-85) cc_final: 0.6132 (tpt90) REVERT: A 169 MET cc_start: 0.6504 (mtt) cc_final: 0.6055 (mtp) REVERT: A 186 GLN cc_start: 0.6027 (tt0) cc_final: 0.5502 (tp40) REVERT: A 205 SER cc_start: 0.7292 (t) cc_final: 0.7072 (p) REVERT: A 207 MET cc_start: 0.7913 (ttt) cc_final: 0.7500 (ttt) REVERT: A 236 GLU cc_start: 0.8295 (tp30) cc_final: 0.8007 (mm-30) REVERT: A 361 LEU cc_start: 0.7738 (tt) cc_final: 0.7041 (mm) outliers start: 19 outliers final: 18 residues processed: 72 average time/residue: 0.0560 time to fit residues: 5.1133 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 71 THR 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 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 339 GLU Chi-restraints excluded: chain A residue 370 ILE 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 Chi-restraints excluded: chain A residue 424 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 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 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 = 0.4366 r_free = 0.4366 target = 0.206508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169670 restraints weight = 4846.543| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.84 r_work: 0.3869 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3429 Z= 0.126 Angle : 0.648 8.424 4645 Z= 0.315 Chirality : 0.036 0.157 535 Planarity : 0.004 0.037 584 Dihedral : 3.818 17.458 465 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.28 % Allowed : 19.17 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.42), residues: 426 helix: 2.92 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -2.30 (0.52), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 386 TYR 0.022 0.001 TYR A 87 PHE 0.028 0.002 PHE A 5 TRP 0.007 0.001 TRP A 409 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3427) covalent geometry : angle 0.64722 ( 4641) SS BOND : bond 0.00156 ( 2) SS BOND : angle 1.34340 ( 4) hydrogen bonds : bond 0.03129 ( 256) hydrogen bonds : angle 3.71073 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 960.28 seconds wall clock time: 17 minutes 9.44 seconds (1029.44 seconds total)