Starting phenix.real_space_refine on Wed Jun 4 10:12:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bix_44603/06_2025/9bix_44603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bix_44603/06_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_44603/06_2025/9bix_44603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bix_44603/06_2025/9bix_44603.map" model { file = "/net/cci-nas-00/data/ceres_data/9bix_44603/06_2025/9bix_44603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bix_44603/06_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-5710/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: 3.34, per 1000 atoms: 1.72 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: 0.46 Conformation dependent library (CDL) restraints added in 238.9 milliseconds 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: 0.29 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: 0.52 Time building geometry restraints manager: 0.55 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.160 Find NCS groups from input model: 0.020 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- 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 : 0.240 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 2.0298 time to fit residues: 51.5203 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 : 0.242 ------------------------------------------------------------------------------- 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: 0.0970 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.105479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082305 restraints weight = 2872.840| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.86 r_work: 0.2973 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1983 Z= 0.174 Angle : 0.606 5.651 2696 Z= 0.334 Chirality : 0.049 0.143 303 Planarity : 0.005 0.040 355 Dihedral : 5.261 25.259 273 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.95 % Allowed : 9.52 % 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: 0.70 (0.54), residues: 240 helix: 1.33 (0.64), residues: 61 sheet: 1.71 (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 0.008 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 0.06397 ( 81) hydrogen bonds : angle 5.15963 ( 243) covalent geometry : bond 0.00397 ( 1983) covalent geometry : angle 0.60597 ( 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 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.242 Fit side-chains REVERT: A 319 LYS cc_start: 0.8631 (mmpt) cc_final: 0.8344 (mmmt) outliers start: 2 outliers final: 0 residues processed: 16 average time/residue: 1.8584 time to fit residues: 30.3489 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 : 0.234 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.104026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081354 restraints weight = 2844.471| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.81 r_work: 0.2949 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 1983 Z= 0.225 Angle : 0.651 5.726 2696 Z= 0.361 Chirality : 0.052 0.144 303 Planarity : 0.006 0.045 355 Dihedral : 5.775 28.504 273 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.95 % Allowed : 11.43 % Favored : 87.62 % 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: 0.38 (0.53), residues: 240 helix: 1.01 (0.62), residues: 63 sheet: 1.37 (0.60), residues: 63 loop : -0.85 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 55 HIS 0.003 0.001 HIS A 314 PHE 0.011 0.003 PHE A 434 TYR 0.008 0.002 TYR A 451 ARG 0.007 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.06676 ( 81) hydrogen bonds : angle 5.06835 ( 243) covalent geometry : bond 0.00535 ( 1983) covalent geometry : angle 0.65099 ( 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 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.231 Fit side-chains REVERT: A 319 LYS cc_start: 0.8617 (mmpt) cc_final: 0.8340 (mmmt) outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 1.8042 time to fit residues: 31.3229 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 : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.107453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085761 restraints weight = 2812.160| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.78 r_work: 0.3036 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1983 Z= 0.101 Angle : 0.504 5.747 2696 Z= 0.275 Chirality : 0.045 0.125 303 Planarity : 0.005 0.042 355 Dihedral : 5.051 24.709 273 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.43 % Allowed : 10.95 % Favored : 87.62 % 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: 0.88 (0.53), residues: 240 helix: 1.81 (0.65), residues: 61 sheet: 1.63 (0.59), residues: 63 loop : -0.72 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 55 HIS 0.003 0.001 HIS A 418 PHE 0.005 0.001 PHE A 434 TYR 0.004 0.001 TYR A 63 ARG 0.002 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 81) hydrogen bonds : angle 4.74929 ( 243) covalent geometry : bond 0.00200 ( 1983) covalent geometry : angle 0.50408 ( 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 : 0.240 Fit side-chains REVERT: A 285 MET cc_start: 0.7018 (tpt) cc_final: 0.6731 (tmm) REVERT: A 319 LYS cc_start: 0.8619 (mmpt) cc_final: 0.8400 (mmmt) outliers start: 3 outliers final: 0 residues processed: 17 average time/residue: 2.0032 time to fit residues: 34.7388 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 : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 0.0060 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.5200 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.108145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.087515 restraints weight = 2850.381| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.66 r_work: 0.3096 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1860 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= 0.138 Angle : 0.556 5.637 2696 Z= 0.306 Chirality : 0.047 0.139 303 Planarity : 0.005 0.044 355 Dihedral : 5.233 25.982 273 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: 0.81 (0.53), residues: 240 helix: 1.55 (0.64), residues: 63 sheet: 1.68 (0.60), residues: 63 loop : -0.74 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 55 HIS 0.002 0.001 HIS A 418 PHE 0.007 0.002 PHE A 434 TYR 0.006 0.001 TYR A 63 ARG 0.003 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 81) hydrogen bonds : angle 4.67739 ( 243) covalent geometry : bond 0.00308 ( 1983) covalent geometry : angle 0.55597 ( 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 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.376 Fit side-chains REVERT: A 319 LYS cc_start: 0.8565 (mmpt) cc_final: 0.8287 (mmmt) outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 2.6196 time to fit residues: 42.7756 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 : 0.247 ------------------------------------------------------------------------------- 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 9 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 0.0970 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.108955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.088405 restraints weight = 2888.710| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.66 r_work: 0.3117 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1972 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= 0.118 Angle : 0.525 5.637 2696 Z= 0.288 Chirality : 0.046 0.133 303 Planarity : 0.005 0.043 355 Dihedral : 5.082 25.246 273 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.43 % Allowed : 12.38 % 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: 0.82 (0.53), residues: 240 helix: 1.60 (0.64), residues: 63 sheet: 1.69 (0.60), residues: 63 loop : -0.76 (0.58), 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 0.04402 ( 81) hydrogen bonds : angle 4.63003 ( 243) covalent geometry : bond 0.00256 ( 1983) covalent geometry : angle 0.52527 ( 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: 3 poor density : 15 time to evaluate : 0.240 Fit side-chains REVERT: A 319 LYS cc_start: 0.8570 (mmpt) cc_final: 0.8292 (mmmt) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 1.7779 time to fit residues: 30.8668 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 : 0.217 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.0170 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.5822 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.109552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.089184 restraints weight = 2853.836| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.64 r_work: 0.3135 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1983 Z= 0.106 Angle : 0.503 5.582 2696 Z= 0.275 Chirality : 0.045 0.131 303 Planarity : 0.005 0.043 355 Dihedral : 4.940 24.332 273 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.58 % Favored : 95.00 % Rotamer: Outliers : 1.43 % Allowed : 12.38 % 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: 0.93 (0.54), residues: 240 helix: 1.63 (0.64), residues: 63 sheet: 1.84 (0.61), residues: 63 loop : -0.72 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.002 0.000 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 290 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 81) hydrogen bonds : angle 4.58570 ( 243) covalent geometry : bond 0.00225 ( 1983) covalent geometry : angle 0.50293 ( 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 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.228 Fit side-chains REVERT: A 285 MET cc_start: 0.6932 (tpt) cc_final: 0.6708 (tmm) REVERT: A 308 ARG cc_start: 0.7098 (tmt170) cc_final: 0.6813 (tpm170) REVERT: A 319 LYS cc_start: 0.8572 (mmpt) cc_final: 0.8294 (mmmt) outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 1.8486 time to fit residues: 30.2080 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 : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.109777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.089228 restraints weight = 2915.017| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.66 r_work: 0.3121 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1983 Z= 0.113 Angle : 0.509 5.584 2696 Z= 0.279 Chirality : 0.046 0.133 303 Planarity : 0.005 0.043 355 Dihedral : 4.979 24.617 273 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.33 % Favored : 96.25 % 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 (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: 0.91 (0.54), residues: 240 helix: 1.62 (0.64), residues: 63 sheet: 1.81 (0.61), residues: 63 loop : -0.72 (0.58), 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 0.002 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 0.04266 ( 81) hydrogen bonds : angle 4.57473 ( 243) covalent geometry : bond 0.00243 ( 1983) covalent geometry : angle 0.50890 ( 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 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.253 Fit side-chains REVERT: A 285 MET cc_start: 0.6926 (tpt) cc_final: 0.6685 (tmm) REVERT: A 319 LYS cc_start: 0.8576 (mmpt) cc_final: 0.8338 (mmmt) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 1.9142 time to fit residues: 31.2838 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 : 0.308 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.110066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.089461 restraints weight = 2988.734| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.68 r_work: 0.3135 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2146 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= 0.100 Angle : 0.493 5.543 2696 Z= 0.269 Chirality : 0.045 0.129 303 Planarity : 0.005 0.043 355 Dihedral : 4.844 23.730 273 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % Rotamer: Outliers : 1.43 % Allowed : 13.81 % 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 (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: 1.01 (0.54), residues: 240 helix: 1.68 (0.64), residues: 63 sheet: 1.97 (0.61), residues: 63 loop : -0.70 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 55 HIS 0.003 0.000 HIS A 418 PHE 0.004 0.001 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 0.03905 ( 81) hydrogen bonds : angle 4.54957 ( 243) covalent geometry : bond 0.00209 ( 1983) covalent geometry : angle 0.49321 ( 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 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.233 Fit side-chains REVERT: A 285 MET cc_start: 0.6908 (tpt) cc_final: 0.6675 (tmm) REVERT: A 308 ARG cc_start: 0.7060 (tmt170) cc_final: 0.6751 (tpm170) REVERT: A 319 LYS cc_start: 0.8576 (mmpt) cc_final: 0.8306 (mmmt) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 1.9774 time to fit residues: 34.2460 Evaluate side-chains 14 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.108313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087490 restraints weight = 2896.582| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.66 r_work: 0.3102 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2067 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= 0.140 Angle : 0.544 5.496 2696 Z= 0.300 Chirality : 0.047 0.139 303 Planarity : 0.005 0.043 355 Dihedral : 5.167 25.774 273 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.75 % Favored : 95.83 % Rotamer: Outliers : 0.95 % Allowed : 14.76 % Favored : 84.29 % 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: 0.76 (0.53), residues: 240 helix: 1.39 (0.63), residues: 63 sheet: 1.79 (0.61), residues: 63 loop : -0.78 (0.58), 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 0.007 0.002 PHE A 434 TYR 0.010 0.001 TYR A 445 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 81) hydrogen bonds : angle 4.61282 ( 243) covalent geometry : bond 0.00314 ( 1983) covalent geometry : angle 0.54426 ( 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 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.246 Fit side-chains REVERT: A 285 MET cc_start: 0.7002 (tpt) cc_final: 0.6750 (tmm) REVERT: A 319 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8311 (mmmt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 2.1935 time to fit residues: 37.9074 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 : 0.231 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.108137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.087318 restraints weight = 2882.048| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.65 r_work: 0.3096 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2081 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= 0.139 Angle : 0.548 5.474 2696 Z= 0.303 Chirality : 0.047 0.137 303 Planarity : 0.005 0.043 355 Dihedral : 5.201 25.976 273 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.58 % Favored : 95.00 % Rotamer: Outliers : 1.43 % Allowed : 13.81 % 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 (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: 0.68 (0.53), residues: 240 helix: 1.24 (0.63), residues: 63 sheet: 1.79 (0.61), residues: 63 loop : -0.81 (0.58), 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 0.007 0.002 PHE A 434 TYR 0.009 0.001 TYR A 445 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04910 ( 81) hydrogen bonds : angle 4.66284 ( 243) covalent geometry : bond 0.00311 ( 1983) covalent geometry : angle 0.54768 ( 2696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.92 seconds wall clock time: 39 minutes 38.82 seconds (2378.82 seconds total)