Starting phenix.real_space_refine on Wed Jun 4 10:34:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bje_44632/06_2025/9bje_44632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bje_44632/06_2025/9bje_44632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bje_44632/06_2025/9bje_44632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bje_44632/06_2025/9bje_44632.map" model { file = "/net/cci-nas-00/data/ceres_data/9bje_44632/06_2025/9bje_44632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bje_44632/06_2025/9bje_44632.cif" } resolution = 2.58 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= 0.002 sd= 0.070 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 1321 2.51 5 N 378 2.21 5 O 389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 2094 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2094 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 18, 'TRANS': 247} Chain breaks: 1 Time building chain proxies: 2.98, per 1000 atoms: 1.42 Number of scatterers: 2094 At special positions: 0 Unit cell: (81.9, 79.17, 70.98, 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 389 8.00 N 378 7.00 C 1321 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: 0.51 Conformation dependent library (CDL) restraints added in 262.4 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 498 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 29.7% alpha, 33.5% 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 18 through 27 Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 280 through 304 removed outlier: 3.748A pdb=" N ILE A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.607A pdb=" N VAL A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.527A pdb=" N HIS A 416 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.527A pdb=" N HIS A 416 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 440 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE A 435 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN A 442 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 62 Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.749A pdb=" N ILE A 319 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 465 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 464 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER A 398 " --> pdb=" O ASP A 464 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 371 97 hydrogen bonds defined for protein. 273 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: 0.54 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 569 1.33 - 1.45: 354 1.45 - 1.57: 1206 1.57 - 1.69: 0 1.69 - 1.81: 11 Bond restraints: 2140 Sorted by residual: bond pdb=" C ARG A 438 " pdb=" O ARG A 438 " ideal model delta sigma weight residual 1.235 1.210 0.025 1.34e-02 5.57e+03 3.62e+00 bond pdb=" CA ARG A 438 " pdb=" CB ARG A 438 " ideal model delta sigma weight residual 1.530 1.502 0.028 1.64e-02 3.72e+03 2.81e+00 bond pdb=" C ARG A 438 " pdb=" N ALA A 439 " ideal model delta sigma weight residual 1.333 1.313 0.020 1.42e-02 4.96e+03 1.92e+00 bond pdb=" CA ARG A 438 " pdb=" C ARG A 438 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.48e-02 4.57e+03 1.67e+00 bond pdb=" CB TRP A 359 " pdb=" CG TRP A 359 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.54e-01 ... (remaining 2135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 2737 1.39 - 2.77: 147 2.77 - 4.16: 23 4.16 - 5.55: 5 5.55 - 6.94: 4 Bond angle restraints: 2916 Sorted by residual: angle pdb=" N TYR A 424 " pdb=" CA TYR A 424 " pdb=" C TYR A 424 " ideal model delta sigma weight residual 111.02 105.39 5.63 1.52e+00 4.33e-01 1.37e+01 angle pdb=" CA LYS A 394 " pdb=" CB LYS A 394 " pdb=" CG LYS A 394 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " pdb=" NE ARG A 296 " ideal model delta sigma weight residual 112.00 118.94 -6.94 2.20e+00 2.07e-01 9.94e+00 angle pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta sigma weight residual 110.67 115.68 -5.01 1.92e+00 2.71e-01 6.80e+00 angle pdb=" N LYS A 394 " pdb=" CA LYS A 394 " pdb=" CB LYS A 394 " ideal model delta sigma weight residual 110.32 106.15 4.17 1.70e+00 3.46e-01 6.01e+00 ... (remaining 2911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 1166 17.19 - 34.38: 98 34.38 - 51.57: 25 51.57 - 68.76: 5 68.76 - 85.94: 3 Dihedral angle restraints: 1297 sinusoidal: 527 harmonic: 770 Sorted by residual: dihedral pdb=" CA LEU A 403 " pdb=" C LEU A 403 " pdb=" N ARG A 404 " pdb=" CA ARG A 404 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CB GLU A 300 " pdb=" CG GLU A 300 " pdb=" CD GLU A 300 " pdb=" OE1 GLU A 300 " ideal model delta sinusoidal sigma weight residual 0.00 -85.94 85.94 1 3.00e+01 1.11e-03 9.91e+00 dihedral pdb=" N GLU A 283 " pdb=" CA GLU A 283 " pdb=" CB GLU A 283 " pdb=" CG GLU A 283 " ideal model delta sinusoidal sigma weight residual -60.00 -114.07 54.07 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 1294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 214 0.041 - 0.081: 84 0.081 - 0.122: 30 0.122 - 0.163: 4 0.163 - 0.203: 1 Chirality restraints: 333 Sorted by residual: chirality pdb=" CA ARG A 296 " pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CB ARG A 296 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL A 453 " pdb=" N VAL A 453 " pdb=" C VAL A 453 " pdb=" CB VAL A 453 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE A 384 " pdb=" N ILE A 384 " pdb=" C ILE A 384 " pdb=" CB ILE A 384 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 330 not shown) Planarity restraints: 379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 425 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 426 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 324 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 325 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 348 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 349 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 349 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 349 " 0.021 5.00e-02 4.00e+02 ... (remaining 376 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 341 2.77 - 3.31: 1877 3.31 - 3.84: 3356 3.84 - 4.37: 4005 4.37 - 4.90: 6822 Nonbonded interactions: 16401 Sorted by model distance: nonbonded pdb=" O LEU A 334 " pdb=" OG1 THR A 337 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP A 332 " pdb=" NH1 ARG A 380 " model vdw 2.249 3.120 nonbonded pdb=" OG1 THR A 327 " pdb=" OD2 ASP A 330 " model vdw 2.374 3.040 nonbonded pdb=" N GLU A 395 " pdb=" OE1 GLU A 395 " model vdw 2.385 3.120 nonbonded pdb=" OG1 THR A 393 " pdb=" OG1 THR A 397 " model vdw 2.391 3.040 ... (remaining 16396 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.730 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.005 0.028 2140 Z= 0.202 Angle : 0.731 6.936 2916 Z= 0.396 Chirality : 0.050 0.203 333 Planarity : 0.006 0.047 379 Dihedral : 14.261 85.944 799 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.88 % Allowed : 4.82 % Favored : 94.30 % 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: 0.30 (0.53), residues: 262 helix: 1.40 (0.60), residues: 76 sheet: 1.21 (0.67), residues: 65 loop : -1.21 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 339 HIS 0.003 0.001 HIS A 311 PHE 0.005 0.002 PHE A 385 TYR 0.017 0.002 TYR A 60 ARG 0.011 0.001 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.13497 ( 92) hydrogen bonds : angle 6.51584 ( 273) covalent geometry : bond 0.00459 ( 2140) covalent geometry : angle 0.73122 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.256 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 1.5107 time to fit residues: 60.0352 Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109456 restraints weight = 2430.891| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.71 r_work: 0.3153 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2140 Z= 0.115 Angle : 0.507 5.461 2916 Z= 0.263 Chirality : 0.043 0.126 333 Planarity : 0.005 0.050 379 Dihedral : 4.280 19.995 294 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.88 % Allowed : 9.21 % Favored : 89.91 % 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: 0.78 (0.51), residues: 262 helix: 1.83 (0.59), residues: 77 sheet: 1.08 (0.65), residues: 65 loop : -0.68 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 339 HIS 0.003 0.001 HIS A 416 PHE 0.006 0.001 PHE A 344 TYR 0.010 0.001 TYR A 60 ARG 0.003 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 92) hydrogen bonds : angle 5.07730 ( 273) covalent geometry : bond 0.00264 ( 2140) covalent geometry : angle 0.50660 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.264 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 1.5771 time to fit residues: 57.7641 Evaluate side-chains 34 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107040 restraints weight = 2432.842| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.71 r_work: 0.3121 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2140 Z= 0.135 Angle : 0.503 5.393 2916 Z= 0.263 Chirality : 0.043 0.129 333 Planarity : 0.005 0.055 379 Dihedral : 4.401 20.812 294 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.32 % Allowed : 10.96 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.51), residues: 262 helix: 1.98 (0.58), residues: 77 sheet: 0.97 (0.63), residues: 65 loop : -0.58 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 52 HIS 0.002 0.001 HIS A 311 PHE 0.006 0.002 PHE A 307 TYR 0.011 0.002 TYR A 60 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 92) hydrogen bonds : angle 5.03013 ( 273) covalent geometry : bond 0.00319 ( 2140) covalent geometry : angle 0.50338 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.250 Fit side-chains REVERT: A 301 MET cc_start: 0.9013 (mmt) cc_final: 0.8728 (mmt) REVERT: A 316 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8074 (mmtt) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 1.5875 time to fit residues: 54.9660 Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 316 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106556 restraints weight = 2378.866| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.68 r_work: 0.3115 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2140 Z= 0.130 Angle : 0.491 5.465 2916 Z= 0.257 Chirality : 0.043 0.127 333 Planarity : 0.005 0.056 379 Dihedral : 4.397 21.216 294 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.88 % Allowed : 14.47 % Favored : 84.65 % 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 (0.51), residues: 262 helix: 1.80 (0.58), residues: 79 sheet: 0.83 (0.61), residues: 70 loop : -0.51 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 52 HIS 0.002 0.000 HIS A 311 PHE 0.006 0.002 PHE A 432 TYR 0.009 0.002 TYR A 60 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 92) hydrogen bonds : angle 4.98239 ( 273) covalent geometry : bond 0.00311 ( 2140) covalent geometry : angle 0.49134 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.270 Fit side-chains REVERT: A 410 GLN cc_start: 0.8830 (mt0) cc_final: 0.8488 (mt0) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 1.6899 time to fit residues: 60.3037 Evaluate side-chains 34 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109073 restraints weight = 2436.885| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.72 r_work: 0.3132 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2140 Z= 0.092 Angle : 0.448 5.383 2916 Z= 0.233 Chirality : 0.041 0.125 333 Planarity : 0.005 0.054 379 Dihedral : 4.152 20.230 294 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.75 % Allowed : 15.35 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.51), residues: 262 helix: 2.38 (0.58), residues: 76 sheet: 0.93 (0.61), residues: 70 loop : -0.54 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 339 HIS 0.002 0.000 HIS A 416 PHE 0.007 0.001 PHE A 432 TYR 0.006 0.001 TYR A 365 ARG 0.002 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 92) hydrogen bonds : angle 4.79582 ( 273) covalent geometry : bond 0.00208 ( 2140) covalent geometry : angle 0.44834 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.252 Fit side-chains REVERT: A 316 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7925 (mmtt) REVERT: A 394 LYS cc_start: 0.8068 (tttp) cc_final: 0.7742 (tttm) REVERT: A 410 GLN cc_start: 0.8808 (mt0) cc_final: 0.8473 (mt0) outliers start: 4 outliers final: 0 residues processed: 33 average time/residue: 1.5211 time to fit residues: 51.1991 Evaluate side-chains 32 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105759 restraints weight = 2410.573| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.70 r_work: 0.3105 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2140 Z= 0.147 Angle : 0.504 5.451 2916 Z= 0.264 Chirality : 0.044 0.128 333 Planarity : 0.005 0.056 379 Dihedral : 4.424 21.633 294 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.32 % Allowed : 16.67 % Favored : 82.02 % 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: 0.98 (0.51), residues: 262 helix: 2.29 (0.58), residues: 76 sheet: 0.79 (0.60), residues: 70 loop : -0.54 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 52 HIS 0.002 0.001 HIS A 311 PHE 0.005 0.002 PHE A 432 TYR 0.009 0.002 TYR A 365 ARG 0.005 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 92) hydrogen bonds : angle 4.97468 ( 273) covalent geometry : bond 0.00353 ( 2140) covalent geometry : angle 0.50441 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.264 Fit side-chains REVERT: A 410 GLN cc_start: 0.8866 (mt0) cc_final: 0.8512 (mt0) outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 1.5696 time to fit residues: 55.9902 Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106311 restraints weight = 2428.712| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.70 r_work: 0.3108 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2140 Z= 0.131 Angle : 0.489 5.453 2916 Z= 0.255 Chirality : 0.043 0.126 333 Planarity : 0.005 0.057 379 Dihedral : 4.379 21.300 294 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.32 % Allowed : 17.11 % Favored : 81.58 % 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: 1.02 (0.51), residues: 262 helix: 2.32 (0.58), residues: 76 sheet: 1.00 (0.61), residues: 68 loop : -0.63 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 52 HIS 0.001 0.000 HIS A 311 PHE 0.005 0.001 PHE A 432 TYR 0.009 0.002 TYR A 365 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 92) hydrogen bonds : angle 4.95261 ( 273) covalent geometry : bond 0.00314 ( 2140) covalent geometry : angle 0.48887 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.247 Fit side-chains REVERT: A 283 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7295 (tp30) REVERT: A 410 GLN cc_start: 0.8857 (mt0) cc_final: 0.8488 (mt0) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 1.7125 time to fit residues: 59.3218 Evaluate side-chains 32 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 0.0370 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109479 restraints weight = 2438.597| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.65 r_work: 0.3144 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2140 Z= 0.090 Angle : 0.451 5.354 2916 Z= 0.235 Chirality : 0.041 0.121 333 Planarity : 0.005 0.054 379 Dihedral : 4.147 20.174 294 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.32 % Allowed : 17.11 % Favored : 81.58 % 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: 1.16 (0.52), residues: 262 helix: 2.60 (0.58), residues: 76 sheet: 0.95 (0.62), residues: 70 loop : -0.60 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 339 HIS 0.002 0.000 HIS A 416 PHE 0.006 0.001 PHE A 432 TYR 0.006 0.001 TYR A 365 ARG 0.002 0.000 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 92) hydrogen bonds : angle 4.73873 ( 273) covalent geometry : bond 0.00203 ( 2140) covalent geometry : angle 0.45060 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.267 Fit side-chains REVERT: A 410 GLN cc_start: 0.8823 (mt0) cc_final: 0.8467 (mt0) outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 1.5262 time to fit residues: 54.4682 Evaluate side-chains 31 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106174 restraints weight = 2458.144| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.72 r_work: 0.3108 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2140 Z= 0.133 Angle : 0.491 5.415 2916 Z= 0.256 Chirality : 0.043 0.126 333 Planarity : 0.005 0.056 379 Dihedral : 4.334 21.214 294 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.44 % Allowed : 17.98 % Favored : 81.58 % 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: 1.09 (0.51), residues: 262 helix: 2.52 (0.58), residues: 76 sheet: 0.86 (0.61), residues: 70 loop : -0.59 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 52 HIS 0.001 0.000 HIS A 311 PHE 0.005 0.001 PHE A 432 TYR 0.010 0.002 TYR A 365 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 92) hydrogen bonds : angle 4.86877 ( 273) covalent geometry : bond 0.00322 ( 2140) covalent geometry : angle 0.49105 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.248 Fit side-chains REVERT: A 410 GLN cc_start: 0.8857 (mt0) cc_final: 0.8488 (mt0) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 1.5455 time to fit residues: 51.9278 Evaluate side-chains 32 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 0.0270 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108570 restraints weight = 2398.473| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.62 r_work: 0.3131 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 2140 Z= 0.099 Angle : 0.460 5.373 2916 Z= 0.239 Chirality : 0.042 0.123 333 Planarity : 0.005 0.054 379 Dihedral : 4.174 20.523 294 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.88 % Allowed : 17.11 % Favored : 82.02 % 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: 1.17 (0.51), residues: 262 helix: 2.63 (0.58), residues: 76 sheet: 0.91 (0.61), residues: 70 loop : -0.58 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 52 HIS 0.002 0.000 HIS A 416 PHE 0.006 0.001 PHE A 432 TYR 0.006 0.001 TYR A 365 ARG 0.002 0.000 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 92) hydrogen bonds : angle 4.77546 ( 273) covalent geometry : bond 0.00231 ( 2140) covalent geometry : angle 0.45998 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.235 Fit side-chains REVERT: A 410 GLN cc_start: 0.8835 (mt0) cc_final: 0.8473 (mt0) outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 1.4913 time to fit residues: 50.2944 Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 3 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105577 restraints weight = 2452.954| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.72 r_work: 0.3076 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2140 Z= 0.143 Angle : 0.501 5.445 2916 Z= 0.261 Chirality : 0.043 0.127 333 Planarity : 0.005 0.056 379 Dihedral : 4.389 21.509 294 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.88 % Allowed : 17.11 % Favored : 82.02 % 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: 1.03 (0.51), residues: 262 helix: 2.45 (0.58), residues: 76 sheet: 0.80 (0.60), residues: 70 loop : -0.60 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 52 HIS 0.001 0.001 HIS A 348 PHE 0.005 0.002 PHE A 307 TYR 0.010 0.002 TYR A 365 ARG 0.003 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 92) hydrogen bonds : angle 4.92777 ( 273) covalent geometry : bond 0.00345 ( 2140) covalent geometry : angle 0.50108 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2800.30 seconds wall clock time: 48 minutes 29.43 seconds (2909.43 seconds total)