Starting phenix.real_space_refine on Wed Sep 17 03:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bix_44603/09_2025/9bix_44603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bix_44603/09_2025/9bix_44603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bix_44603/09_2025/9bix_44603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bix_44603/09_2025/9bix_44603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bix_44603/09_2025/9bix_44603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bix_44603/09_2025/9bix_44603.map" } resolution = 2.59 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= 0.019 sd= 0.116 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 6 5.16 5 C 1219 2.51 5 N 362 2.21 5 O 357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1944 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1944 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 15, 'TRANS': 228} Chain breaks: 1 Time building chain proxies: 0.79, per 1000 atoms: 0.41 Number of scatterers: 1944 At special positions: 0 Unit cell: (60.48, 75.6, 71.4, 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 6 16.00 O 357 8.00 N 362 7.00 C 1219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.16 Conformation dependent library (CDL) restraints added in 79.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 454 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 4 sheets defined 28.3% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 283 through 307 removed outlier: 3.708A pdb=" N ILE A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 57 removed outlier: 6.821A pdb=" N VAL A 442 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE A 437 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLN A 444 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET A 435 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 427 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 432 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU A 425 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 8.170A pdb=" N ILE A 322 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL A 467 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP A 466 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER A 400 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 346 " --> pdb=" O MET A 405 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 347 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 379 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ASP A 377 " --> pdb=" O PRO A 388 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 243 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: 0.27 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 343 1.32 - 1.44: 492 1.44 - 1.56: 1137 1.56 - 1.69: 0 1.69 - 1.81: 11 Bond restraints: 1983 Sorted by residual: bond pdb=" C PRO A 331 " pdb=" O PRO A 331 " ideal model delta sigma weight residual 1.238 1.200 0.038 1.24e-02 6.50e+03 9.22e+00 bond pdb=" C THR A 330 " pdb=" O THR A 330 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.37e-02 5.33e+03 5.38e+00 bond pdb=" CA PRO A 331 " pdb=" C PRO A 331 " ideal model delta sigma weight residual 1.516 1.551 -0.034 1.61e-02 3.86e+03 4.54e+00 bond pdb=" C ARG A 308 " pdb=" O ARG A 308 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.31e-02 5.83e+03 2.55e+00 bond pdb=" C PRO A 329 " pdb=" O PRO A 329 " ideal model delta sigma weight residual 1.235 1.217 0.018 1.30e-02 5.92e+03 1.94e+00 ... (remaining 1978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 2573 1.05 - 2.11: 92 2.11 - 3.16: 24 3.16 - 4.21: 5 4.21 - 5.26: 2 Bond angle restraints: 2696 Sorted by residual: angle pdb=" O PRO A 328 " pdb=" C PRO A 328 " pdb=" N PRO A 329 " ideal model delta sigma weight residual 121.15 122.74 -1.59 4.70e-01 4.53e+00 1.14e+01 angle pdb=" C THR A 330 " pdb=" CA THR A 330 " pdb=" CB THR A 330 " ideal model delta sigma weight residual 109.37 114.35 -4.98 1.59e+00 3.96e-01 9.82e+00 angle pdb=" N THR A 330 " pdb=" CA THR A 330 " pdb=" CB THR A 330 " ideal model delta sigma weight residual 109.74 106.55 3.19 1.16e+00 7.43e-01 7.58e+00 angle pdb=" C PRO A 331 " pdb=" N ASP A 332 " pdb=" CA ASP A 332 " ideal model delta sigma weight residual 120.29 123.97 -3.68 1.42e+00 4.96e-01 6.70e+00 angle pdb=" CA PRO A 328 " pdb=" C PRO A 328 " pdb=" N PRO A 329 " ideal model delta sigma weight residual 118.06 116.29 1.77 8.30e-01 1.45e+00 4.52e+00 ... (remaining 2691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 1134 16.72 - 33.43: 59 33.43 - 50.15: 12 50.15 - 66.86: 1 66.86 - 83.58: 2 Dihedral angle restraints: 1208 sinusoidal: 504 harmonic: 704 Sorted by residual: dihedral pdb=" CA LEU A 464 " pdb=" C LEU A 464 " pdb=" N GLU A 465 " pdb=" CA GLU A 465 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 83.58 -83.58 1 3.00e+01 1.11e-03 9.47e+00 dihedral pdb=" CB LYS A 319 " pdb=" CG LYS A 319 " pdb=" CD LYS A 319 " pdb=" CE LYS A 319 " ideal model delta sinusoidal sigma weight residual 60.00 112.68 -52.68 3 1.50e+01 4.44e-03 9.14e+00 ... (remaining 1205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 166 0.027 - 0.055: 72 0.055 - 0.082: 33 0.082 - 0.109: 16 0.109 - 0.136: 16 Chirality restraints: 303 Sorted by residual: chirality pdb=" CA ILE A 437 " pdb=" N ILE A 437 " pdb=" C ILE A 437 " pdb=" CB ILE A 437 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA PRO A 423 " pdb=" N PRO A 423 " pdb=" C PRO A 423 " pdb=" CB PRO A 423 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA THR A 330 " pdb=" N THR A 330 " pdb=" C THR A 330 " pdb=" CB THR A 330 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 300 not shown) Planarity restraints: 355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 328 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C PRO A 328 " -0.026 2.00e-02 2.50e+03 pdb=" O PRO A 328 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO A 329 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 330 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C THR A 330 " 0.026 2.00e-02 2.50e+03 pdb=" O THR A 330 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO A 331 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 330 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 331 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " -0.020 5.00e-02 4.00e+02 ... (remaining 352 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 231 2.76 - 3.29: 1746 3.29 - 3.83: 2961 3.83 - 4.36: 3686 4.36 - 4.90: 6289 Nonbonded interactions: 14913 Sorted by model distance: nonbonded pdb=" OG1 THR A 395 " pdb=" OG1 THR A 399 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR A 324 " pdb=" O SER A 326 " model vdw 2.266 3.040 nonbonded pdb=" NH2 ARG A 352 " pdb=" OE1 GLN A 398 " model vdw 2.332 3.120 nonbonded pdb=" OD2 ASP A 286 " pdb=" NH1 ARG A 290 " model vdw 2.374 3.120 nonbonded pdb=" NH1 ARG A 47 " pdb=" OE2 GLU A 298 " model vdw 2.397 3.120 ... (remaining 14908 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: 7.280 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.390 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1983 Z= 0.170 Angle : 0.518 5.264 2696 Z= 0.301 Chirality : 0.047 0.136 303 Planarity : 0.004 0.036 355 Dihedral : 11.106 83.580 754 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.95 % Allowed : 2.86 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.54), residues: 240 helix: 0.14 (0.60), residues: 61 sheet: 1.70 (0.61), residues: 67 loop : -0.53 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 382 TYR 0.006 0.001 TYR A 63 PHE 0.006 0.002 PHE A 434 TRP 0.009 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 1983) covalent geometry : angle 0.51770 ( 2696) hydrogen bonds : bond 0.23883 ( 81) hydrogen bonds : angle 6.85935 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.079 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 1.0721 time to fit residues: 27.1242 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084377 restraints weight = 2897.789| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.86 r_work: 0.3013 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1983 Z= 0.131 Angle : 0.560 5.654 2696 Z= 0.306 Chirality : 0.047 0.135 303 Planarity : 0.005 0.037 355 Dihedral : 4.982 23.521 273 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.48 % Allowed : 9.52 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.54), residues: 240 helix: 1.48 (0.64), residues: 61 sheet: 1.93 (0.61), residues: 63 loop : -0.65 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.004 0.001 TYR A 63 PHE 0.005 0.001 PHE A 434 TRP 0.011 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 1983) covalent geometry : angle 0.55983 ( 2696) hydrogen bonds : bond 0.05174 ( 81) hydrogen bonds : angle 5.03316 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.083 Fit side-chains REVERT: A 319 LYS cc_start: 0.8621 (mmpt) cc_final: 0.8345 (mmmt) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.8411 time to fit residues: 13.7265 Evaluate side-chains 13 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.086993 restraints weight = 2875.684| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.81 r_work: 0.3058 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1983 Z= 0.094 Angle : 0.486 5.722 2696 Z= 0.265 Chirality : 0.045 0.126 303 Planarity : 0.004 0.038 355 Dihedral : 4.719 22.214 273 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.48 % Allowed : 11.43 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.55), residues: 240 helix: 1.98 (0.66), residues: 61 sheet: 2.09 (0.61), residues: 63 loop : -0.47 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 382 TYR 0.004 0.001 TYR A 63 PHE 0.004 0.001 PHE A 434 TRP 0.008 0.001 TRP A 55 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 1983) covalent geometry : angle 0.48604 ( 2696) hydrogen bonds : bond 0.03910 ( 81) hydrogen bonds : angle 4.65501 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.8640 (mmpt) cc_final: 0.8365 (mmmt) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.9678 time to fit residues: 15.7355 Evaluate side-chains 15 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.084961 restraints weight = 2874.431| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.66 r_work: 0.3058 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 1983 Z= 0.243 Angle : 0.652 5.627 2696 Z= 0.360 Chirality : 0.053 0.150 303 Planarity : 0.006 0.047 355 Dihedral : 5.694 27.950 273 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.43 % Allowed : 11.90 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.53), residues: 240 helix: 1.16 (0.62), residues: 63 sheet: 1.69 (0.60), residues: 63 loop : -0.76 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 382 TYR 0.009 0.002 TYR A 451 PHE 0.011 0.004 PHE A 434 TRP 0.012 0.002 TRP A 55 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 1983) covalent geometry : angle 0.65248 ( 2696) hydrogen bonds : bond 0.06608 ( 81) hydrogen bonds : angle 5.00672 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.086 Fit side-chains REVERT: A 319 LYS cc_start: 0.8593 (mmpt) cc_final: 0.8301 (mmmt) outliers start: 3 outliers final: 0 residues processed: 16 average time/residue: 0.9477 time to fit residues: 15.4140 Evaluate side-chains 14 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.105270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083254 restraints weight = 2830.219| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.78 r_work: 0.2993 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1983 Z= 0.143 Angle : 0.554 5.646 2696 Z= 0.304 Chirality : 0.047 0.139 303 Planarity : 0.005 0.044 355 Dihedral : 5.388 26.698 273 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.43 % Allowed : 11.43 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.53), residues: 240 helix: 1.34 (0.63), residues: 63 sheet: 1.74 (0.60), residues: 63 loop : -0.74 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.006 0.001 TYR A 451 PHE 0.008 0.002 PHE A 434 TRP 0.012 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 1983) covalent geometry : angle 0.55396 ( 2696) hydrogen bonds : bond 0.05144 ( 81) hydrogen bonds : angle 4.78984 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.085 Fit side-chains REVERT: A 319 LYS cc_start: 0.8616 (mmpt) cc_final: 0.8383 (mmmt) outliers start: 3 outliers final: 1 residues processed: 16 average time/residue: 1.0531 time to fit residues: 17.0974 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084711 restraints weight = 2866.357| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.79 r_work: 0.3022 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1983 Z= 0.112 Angle : 0.514 5.638 2696 Z= 0.281 Chirality : 0.046 0.132 303 Planarity : 0.005 0.044 355 Dihedral : 5.086 24.930 273 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.17 % Favored : 95.42 % Rotamer: Outliers : 1.43 % Allowed : 11.90 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.54), residues: 240 helix: 1.57 (0.64), residues: 63 sheet: 1.89 (0.60), residues: 63 loop : -0.69 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.005 0.001 TYR A 451 PHE 0.006 0.002 PHE A 434 TRP 0.011 0.001 TRP A 55 HIS 0.002 0.000 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 1983) covalent geometry : angle 0.51418 ( 2696) hydrogen bonds : bond 0.04302 ( 81) hydrogen bonds : angle 4.60746 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.085 Fit side-chains REVERT: A 285 MET cc_start: 0.6922 (tpt) cc_final: 0.6670 (tmm) REVERT: A 319 LYS cc_start: 0.8646 (mmpt) cc_final: 0.8430 (mmmt) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.9685 time to fit residues: 16.7223 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.085796 restraints weight = 2827.589| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.65 r_work: 0.3062 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 1983 Z= 0.203 Angle : 0.620 5.546 2696 Z= 0.343 Chirality : 0.050 0.150 303 Planarity : 0.006 0.046 355 Dihedral : 5.636 28.148 273 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.48 % Allowed : 12.86 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.53), residues: 240 helix: 1.11 (0.62), residues: 63 sheet: 1.66 (0.60), residues: 63 loop : -0.87 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 382 TYR 0.008 0.002 TYR A 451 PHE 0.010 0.003 PHE A 434 TRP 0.011 0.002 TRP A 55 HIS 0.002 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 1983) covalent geometry : angle 0.62031 ( 2696) hydrogen bonds : bond 0.06121 ( 81) hydrogen bonds : angle 4.84863 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.096 Fit side-chains REVERT: A 319 LYS cc_start: 0.8577 (mmpt) cc_final: 0.8292 (mmmt) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.9599 time to fit residues: 16.5898 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.085530 restraints weight = 2857.323| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.67 r_work: 0.3066 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1983 Z= 0.190 Angle : 0.606 5.516 2696 Z= 0.335 Chirality : 0.049 0.145 303 Planarity : 0.006 0.046 355 Dihedral : 5.607 27.972 273 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.95 % Allowed : 13.33 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.52), residues: 240 helix: 0.98 (0.62), residues: 63 sheet: 1.55 (0.59), residues: 63 loop : -0.97 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 382 TYR 0.008 0.001 TYR A 451 PHE 0.009 0.003 PHE A 434 TRP 0.011 0.002 TRP A 55 HIS 0.002 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 1983) covalent geometry : angle 0.60622 ( 2696) hydrogen bonds : bond 0.05827 ( 81) hydrogen bonds : angle 4.83628 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.083 Fit side-chains REVERT: A 285 MET cc_start: 0.7063 (tpt) cc_final: 0.6836 (tmm) REVERT: A 319 LYS cc_start: 0.8562 (mmpt) cc_final: 0.8294 (mmmt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.8927 time to fit residues: 15.4509 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.086600 restraints weight = 2802.316| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.64 r_work: 0.3085 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1983 Z= 0.149 Angle : 0.566 5.511 2696 Z= 0.312 Chirality : 0.048 0.140 303 Planarity : 0.005 0.046 355 Dihedral : 5.439 27.082 273 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.83 % Favored : 93.75 % Rotamer: Outliers : 0.95 % Allowed : 14.29 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.53), residues: 240 helix: 1.16 (0.63), residues: 63 sheet: 1.68 (0.60), residues: 63 loop : -0.94 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.006 0.001 TYR A 451 PHE 0.008 0.002 PHE A 434 TRP 0.012 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 1983) covalent geometry : angle 0.56557 ( 2696) hydrogen bonds : bond 0.05180 ( 81) hydrogen bonds : angle 4.75521 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.049 Fit side-chains REVERT: A 285 MET cc_start: 0.7016 (tpt) cc_final: 0.6797 (tmm) REVERT: A 319 LYS cc_start: 0.8561 (mmpt) cc_final: 0.8321 (mmmt) outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 1.0191 time to fit residues: 16.5507 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086200 restraints weight = 2910.971| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.68 r_work: 0.3082 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1983 Z= 0.156 Angle : 0.569 5.445 2696 Z= 0.314 Chirality : 0.048 0.141 303 Planarity : 0.006 0.047 355 Dihedral : 5.467 27.428 273 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.42 % Favored : 94.17 % Rotamer: Outliers : 0.48 % Allowed : 14.76 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.53), residues: 240 helix: 1.15 (0.63), residues: 63 sheet: 1.64 (0.60), residues: 63 loop : -0.89 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.007 0.001 TYR A 451 PHE 0.008 0.002 PHE A 434 TRP 0.012 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 1983) covalent geometry : angle 0.56942 ( 2696) hydrogen bonds : bond 0.05286 ( 81) hydrogen bonds : angle 4.78135 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.051 Fit side-chains REVERT: A 285 MET cc_start: 0.7048 (tpt) cc_final: 0.6822 (tmm) REVERT: A 319 LYS cc_start: 0.8559 (mmpt) cc_final: 0.8308 (mmmt) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.9594 time to fit residues: 15.5575 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087295 restraints weight = 2881.505| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.67 r_work: 0.3098 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1983 Z= 0.130 Angle : 0.538 5.477 2696 Z= 0.296 Chirality : 0.047 0.135 303 Planarity : 0.005 0.046 355 Dihedral : 5.283 26.179 273 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.58 % Favored : 95.00 % Rotamer: Outliers : 0.95 % Allowed : 14.29 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.53), residues: 240 helix: 1.35 (0.64), residues: 63 sheet: 1.76 (0.60), residues: 63 loop : -0.85 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.005 0.001 TYR A 451 PHE 0.007 0.002 PHE A 434 TRP 0.012 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 1983) covalent geometry : angle 0.53757 ( 2696) hydrogen bonds : bond 0.04697 ( 81) hydrogen bonds : angle 4.68023 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1130.15 seconds wall clock time: 19 minutes 52.29 seconds (1192.29 seconds total)