Starting phenix.real_space_refine on Fri May 9 13:11:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bix_44603/05_2025/9bix_44603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bix_44603/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bix_44603/05_2025/9bix_44603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bix_44603/05_2025/9bix_44603.map" model { file = "/net/cci-nas-00/data/ceres_data/9bix_44603/05_2025/9bix_44603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bix_44603/05_2025/9bix_44603.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.95, per 1000 atoms: 1.52 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: 0.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.27 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: 0.48 Time building geometry restraints manager: 0.53 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (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 TRP 0.009 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 PHE 0.006 0.002 PHE A 434 TYR 0.006 0.001 TYR A 63 ARG 0.002 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.23883 ( 81) hydrogen bonds : angle 6.85935 ( 243) covalent geometry : bond 0.00318 ( 1983) covalent geometry : angle 0.51770 ( 2696) *********************** 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 : 0.225 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 1.9642 time to fit residues: 49.8609 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 : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.105744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082601 restraints weight = 2873.929| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.86 r_work: 0.2978 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1983 Z= 0.165 Angle : 0.600 5.680 2696 Z= 0.329 Chirality : 0.049 0.142 303 Planarity : 0.005 0.040 355 Dihedral : 5.255 25.315 273 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.48 % Allowed : 10.00 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.54), residues: 240 helix: 1.34 (0.64), residues: 61 sheet: 1.75 (0.60), residues: 63 loop : -0.75 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 55 HIS 0.002 0.001 HIS A 314 PHE 0.007 0.002 PHE A 434 TYR 0.006 0.001 TYR A 451 ARG 0.005 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.06060 ( 81) hydrogen bonds : angle 5.12211 ( 243) covalent geometry : bond 0.00375 ( 1983) covalent geometry : angle 0.60020 ( 2696) *********************** 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 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.229 Fit side-chains REVERT: A 319 LYS cc_start: 0.8633 (mmpt) cc_final: 0.8353 (mmmt) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 1.8596 time to fit residues: 30.3228 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.104100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081423 restraints weight = 2844.088| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.81 r_work: 0.2947 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 1983 Z= 0.219 Angle : 0.642 5.694 2696 Z= 0.357 Chirality : 0.051 0.148 303 Planarity : 0.006 0.045 355 Dihedral : 5.739 28.368 273 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.43 % Allowed : 10.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.53), residues: 240 helix: 1.07 (0.62), residues: 63 sheet: 1.41 (0.60), residues: 63 loop : -0.84 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 55 HIS 0.002 0.001 HIS A 314 PHE 0.011 0.003 PHE A 434 TYR 0.008 0.002 TYR A 451 ARG 0.006 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.06601 ( 81) hydrogen bonds : angle 5.07889 ( 243) covalent geometry : bond 0.00518 ( 1983) covalent geometry : angle 0.64201 ( 2696) *********************** 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 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.208 Fit side-chains REVERT: A 319 LYS cc_start: 0.8613 (mmpt) cc_final: 0.8369 (mmmt) outliers start: 3 outliers final: 0 residues processed: 16 average time/residue: 1.8250 time to fit residues: 29.7923 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 : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.106116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084243 restraints weight = 2808.226| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.78 r_work: 0.3009 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1983 Z= 0.122 Angle : 0.530 5.739 2696 Z= 0.292 Chirality : 0.046 0.134 303 Planarity : 0.005 0.043 355 Dihedral : 5.252 26.059 273 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.43 % Allowed : 10.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.53), residues: 240 helix: 1.45 (0.64), residues: 63 sheet: 1.62 (0.60), residues: 63 loop : -0.75 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.003 0.001 HIS A 418 PHE 0.007 0.002 PHE A 434 TYR 0.005 0.001 TYR A 63 ARG 0.003 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 81) hydrogen bonds : angle 4.81788 ( 243) covalent geometry : bond 0.00261 ( 1983) covalent geometry : angle 0.53018 ( 2696) *********************** 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 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.237 Fit side-chains REVERT: A 319 LYS cc_start: 0.8609 (mmpt) cc_final: 0.8385 (mmmt) outliers start: 3 outliers final: 1 residues processed: 18 average time/residue: 1.7859 time to fit residues: 32.7946 Evaluate side-chains 15 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.4980 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.106585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084637 restraints weight = 2817.352| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.79 r_work: 0.3020 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1874 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= 0.116 Angle : 0.519 5.672 2696 Z= 0.285 Chirality : 0.046 0.135 303 Planarity : 0.005 0.044 355 Dihedral : 5.096 25.132 273 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.53), residues: 240 helix: 1.61 (0.65), residues: 63 sheet: 1.71 (0.60), residues: 63 loop : -0.70 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.003 0.001 HIS A 418 PHE 0.005 0.002 PHE A 434 TYR 0.005 0.001 TYR A 63 ARG 0.002 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 81) hydrogen bonds : angle 4.67509 ( 243) covalent geometry : bond 0.00249 ( 1983) covalent geometry : angle 0.51922 ( 2696) *********************** 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 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.230 Fit side-chains REVERT: A 319 LYS cc_start: 0.8608 (mmpt) cc_final: 0.8390 (mmmt) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 1.7149 time to fit residues: 33.2578 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR 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 9 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.107154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085123 restraints weight = 2853.189| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.80 r_work: 0.3027 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1983 Z= 0.107 Angle : 0.504 5.651 2696 Z= 0.276 Chirality : 0.045 0.132 303 Planarity : 0.005 0.043 355 Dihedral : 4.961 24.361 273 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.95 % Allowed : 12.86 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.54), residues: 240 helix: 1.67 (0.65), residues: 63 sheet: 1.85 (0.60), residues: 63 loop : -0.68 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 PHE 0.005 0.001 PHE A 434 TYR 0.005 0.001 TYR A 63 ARG 0.002 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 81) hydrogen bonds : angle 4.60103 ( 243) covalent geometry : bond 0.00224 ( 1983) covalent geometry : angle 0.50363 ( 2696) *********************** 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 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.210 Fit side-chains REVERT: A 285 MET cc_start: 0.6928 (tpt) cc_final: 0.6689 (tmm) REVERT: A 319 LYS cc_start: 0.8634 (mmpt) cc_final: 0.8420 (mmmt) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 1.7319 time to fit residues: 31.8002 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 : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 447 VAL 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 18 optimal weight: 7.9990 chunk 9 optimal weight: 0.0000 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.108671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088197 restraints weight = 2833.706| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.65 r_work: 0.3111 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1983 Z= 0.123 Angle : 0.522 5.595 2696 Z= 0.287 Chirality : 0.046 0.136 303 Planarity : 0.005 0.043 355 Dihedral : 5.086 25.066 273 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.54), residues: 240 helix: 1.56 (0.64), residues: 63 sheet: 1.78 (0.60), residues: 63 loop : -0.72 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 PHE 0.006 0.002 PHE A 434 TYR 0.005 0.001 TYR A 63 ARG 0.003 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 81) hydrogen bonds : angle 4.61328 ( 243) covalent geometry : bond 0.00270 ( 1983) covalent geometry : angle 0.52198 ( 2696) *********************** 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 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.226 Fit side-chains REVERT: A 319 LYS cc_start: 0.8573 (mmpt) cc_final: 0.8335 (mmmt) outliers start: 3 outliers final: 3 residues processed: 19 average time/residue: 1.9479 time to fit residues: 37.6685 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.108774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086993 restraints weight = 2866.328| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.80 r_work: 0.3069 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1983 Z= 0.092 Angle : 0.492 5.622 2696 Z= 0.268 Chirality : 0.045 0.126 303 Planarity : 0.005 0.043 355 Dihedral : 4.761 23.172 273 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.17 % Favored : 95.42 % Rotamer: Outliers : 0.95 % Allowed : 12.86 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.54), residues: 240 helix: 1.73 (0.65), residues: 63 sheet: 1.96 (0.60), residues: 63 loop : -0.64 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 55 HIS 0.003 0.000 HIS A 418 PHE 0.003 0.001 PHE A 434 TYR 0.004 0.001 TYR A 63 ARG 0.003 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 81) hydrogen bonds : angle 4.57176 ( 243) covalent geometry : bond 0.00184 ( 1983) covalent geometry : angle 0.49168 ( 2696) *********************** 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 : 0.210 Fit side-chains REVERT: A 285 MET cc_start: 0.6841 (tpt) cc_final: 0.6628 (tmm) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 1.9034 time to fit residues: 32.9577 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 : 0.206 ------------------------------------------------------------------------------- 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 1 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 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 = 0.3565 r_free = 0.3565 target = 0.108755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088055 restraints weight = 2960.165| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.68 r_work: 0.3109 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1983 Z= 0.131 Angle : 0.543 5.522 2696 Z= 0.296 Chirality : 0.046 0.135 303 Planarity : 0.005 0.043 355 Dihedral : 5.042 24.879 273 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % Rotamer: Outliers : 0.95 % Allowed : 13.81 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.54), residues: 240 helix: 1.56 (0.64), residues: 63 sheet: 1.89 (0.60), residues: 63 loop : -0.64 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 PHE 0.006 0.002 PHE A 434 TYR 0.005 0.001 TYR A 63 ARG 0.003 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 81) hydrogen bonds : angle 4.62930 ( 243) covalent geometry : bond 0.00297 ( 1983) covalent geometry : angle 0.54302 ( 2696) *********************** 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 : 0.183 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 1.9890 time to fit residues: 34.3889 Evaluate side-chains 15 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.108291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087599 restraints weight = 2903.932| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.67 r_work: 0.3094 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1983 Z= 0.150 Angle : 0.583 6.061 2696 Z= 0.318 Chirality : 0.047 0.139 303 Planarity : 0.005 0.043 355 Dihedral : 5.238 26.198 273 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.33 % Favored : 96.25 % Rotamer: Outliers : 0.95 % Allowed : 13.81 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.53), residues: 240 helix: 1.27 (0.64), residues: 63 sheet: 1.77 (0.60), residues: 63 loop : -0.71 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 55 HIS 0.002 0.001 HIS A 271 PHE 0.007 0.002 PHE A 434 TYR 0.006 0.001 TYR A 451 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.05038 ( 81) hydrogen bonds : angle 4.72843 ( 243) covalent geometry : bond 0.00346 ( 1983) covalent geometry : angle 0.58306 ( 2696) ********************** 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: 2 poor density : 14 time to evaluate : 0.241 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 2.1478 time to fit residues: 34.9918 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 : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.109162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088721 restraints weight = 2899.400| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.65 r_work: 0.3121 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1983 Z= 0.119 Angle : 0.557 7.802 2696 Z= 0.300 Chirality : 0.046 0.130 303 Planarity : 0.005 0.043 355 Dihedral : 5.002 24.571 273 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.58 % Favored : 95.00 % Rotamer: Outliers : 0.95 % Allowed : 13.81 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.54), residues: 240 helix: 1.30 (0.65), residues: 63 sheet: 1.81 (0.60), residues: 63 loop : -0.67 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 PHE 0.005 0.001 PHE A 434 TYR 0.004 0.001 TYR A 63 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 81) hydrogen bonds : angle 4.66850 ( 243) covalent geometry : bond 0.00265 ( 1983) covalent geometry : angle 0.55693 ( 2696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.57 seconds wall clock time: 39 minutes 41.08 seconds (2381.08 seconds total)