Starting phenix.real_space_refine on Fri Aug 22 12:40:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bje_44632/08_2025/9bje_44632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bje_44632/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bje_44632/08_2025/9bje_44632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bje_44632/08_2025/9bje_44632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bje_44632/08_2025/9bje_44632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bje_44632/08_2025/9bje_44632.map" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.14, per 1000 atoms: 0.54 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: 0.29 Conformation dependent library (CDL) restraints added in 140.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.13 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: 0.42 Time building geometry restraints manager: 0.38 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: 6.340 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: 0.010 Process input model: 6.430 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:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (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 ARG 0.011 0.001 ARG A 296 TYR 0.017 0.002 TYR A 60 PHE 0.005 0.002 PHE A 385 TRP 0.013 0.002 TRP A 339 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 2140) covalent geometry : angle 0.73122 ( 2916) hydrogen bonds : bond 0.13497 ( 92) hydrogen bonds : angle 6.51584 ( 273) *********************** 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 : 0.105 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.7323 time to fit residues: 29.0621 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 : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.139571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109644 restraints weight = 2479.814| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.72 r_work: 0.3164 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1172 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= 0.111 Angle : 0.503 5.436 2916 Z= 0.261 Chirality : 0.043 0.124 333 Planarity : 0.005 0.049 379 Dihedral : 4.236 19.802 294 Min Nonbonded Distance : 2.624 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.52), residues: 262 helix: 1.90 (0.60), residues: 76 sheet: 1.10 (0.65), residues: 65 loop : -0.55 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 362 TYR 0.010 0.001 TYR A 60 PHE 0.006 0.001 PHE A 307 TRP 0.005 0.001 TRP A 339 HIS 0.003 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 2140) covalent geometry : angle 0.50262 ( 2916) hydrogen bonds : bond 0.03565 ( 92) hydrogen bonds : angle 5.07832 ( 273) *********************** 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 : 0.096 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.8194 time to fit residues: 29.9773 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 : 0.090 ------------------------------------------------------------------------------- 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 22 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103566 restraints weight = 2452.684| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.71 r_work: 0.3039 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 2140 Z= 0.244 Angle : 0.620 6.653 2916 Z= 0.325 Chirality : 0.049 0.137 333 Planarity : 0.007 0.059 379 Dihedral : 4.892 22.924 294 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.75 % Allowed : 10.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.50), residues: 262 helix: 1.89 (0.58), residues: 74 sheet: 1.01 (0.63), residues: 63 loop : -0.68 (0.53), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 380 TYR 0.015 0.003 TYR A 60 PHE 0.007 0.002 PHE A 344 TRP 0.008 0.002 TRP A 52 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 2140) covalent geometry : angle 0.62012 ( 2916) hydrogen bonds : bond 0.05296 ( 92) hydrogen bonds : angle 5.38227 ( 273) *********************** 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 34 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.087 Fit side-chains REVERT: A 410 GLN cc_start: 0.8902 (mt0) cc_final: 0.8542 (mt0) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.8521 time to fit residues: 26.8616 Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.091 ------------------------------------------------------------------------------- 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 2 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107723 restraints weight = 2441.375| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.71 r_work: 0.3134 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2140 Z= 0.100 Angle : 0.469 5.480 2916 Z= 0.243 Chirality : 0.042 0.126 333 Planarity : 0.005 0.057 379 Dihedral : 4.347 20.756 294 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.88 % Allowed : 14.91 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.51), residues: 262 helix: 1.72 (0.58), residues: 79 sheet: 0.86 (0.61), residues: 70 loop : -0.47 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 380 TYR 0.005 0.001 TYR A 60 PHE 0.007 0.002 PHE A 307 TRP 0.007 0.001 TRP A 339 HIS 0.002 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2140) covalent geometry : angle 0.46879 ( 2916) hydrogen bonds : bond 0.03218 ( 92) hydrogen bonds : angle 4.96884 ( 273) *********************** 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 38 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.090 Fit side-chains REVERT: A 410 GLN cc_start: 0.8835 (mt0) cc_final: 0.8484 (mt0) outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.8204 time to fit residues: 30.8405 Evaluate side-chains 34 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.139301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109492 restraints weight = 2449.477| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.72 r_work: 0.3161 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1828 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= 0.088 Angle : 0.446 5.357 2916 Z= 0.231 Chirality : 0.041 0.125 333 Planarity : 0.005 0.052 379 Dihedral : 4.103 20.082 294 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.88 % Allowed : 16.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.52), residues: 262 helix: 2.43 (0.58), residues: 76 sheet: 0.96 (0.62), residues: 70 loop : -0.49 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 380 TYR 0.005 0.001 TYR A 365 PHE 0.007 0.001 PHE A 432 TRP 0.005 0.001 TRP A 339 HIS 0.002 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 2140) covalent geometry : angle 0.44644 ( 2916) hydrogen bonds : bond 0.02915 ( 92) hydrogen bonds : angle 4.76222 ( 273) *********************** 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: 2 poor density : 33 time to evaluate : 0.088 Fit side-chains REVERT: A 410 GLN cc_start: 0.8833 (mt0) cc_final: 0.8487 (mt0) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.8464 time to fit residues: 30.0753 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.134420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104115 restraints weight = 2407.134| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.70 r_work: 0.3054 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2140 Z= 0.212 Angle : 0.567 6.123 2916 Z= 0.296 Chirality : 0.046 0.131 333 Planarity : 0.006 0.059 379 Dihedral : 4.644 22.272 294 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.75 % Allowed : 15.79 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.50), residues: 262 helix: 1.98 (0.58), residues: 77 sheet: 0.93 (0.60), residues: 68 loop : -0.63 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 380 TYR 0.012 0.002 TYR A 365 PHE 0.006 0.002 PHE A 344 TRP 0.012 0.002 TRP A 52 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 2140) covalent geometry : angle 0.56701 ( 2916) hydrogen bonds : bond 0.04642 ( 92) hydrogen bonds : angle 5.13851 ( 273) *********************** 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 41 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.082 Fit side-chains REVERT: A 296 ARG cc_start: 0.8380 (ttm170) cc_final: 0.8155 (ttm170) REVERT: A 316 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8026 (mtpt) REVERT: A 410 GLN cc_start: 0.8891 (mt0) cc_final: 0.8518 (mt0) outliers start: 4 outliers final: 1 residues processed: 39 average time/residue: 0.7441 time to fit residues: 29.4848 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 : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 316 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108300 restraints weight = 2440.800| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.71 r_work: 0.3117 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2140 Z= 0.095 Angle : 0.467 5.387 2916 Z= 0.243 Chirality : 0.042 0.122 333 Planarity : 0.005 0.056 379 Dihedral : 4.209 20.570 294 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.49 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.51), residues: 262 helix: 2.44 (0.58), residues: 76 sheet: 0.87 (0.61), residues: 70 loop : -0.57 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 380 TYR 0.005 0.001 TYR A 365 PHE 0.007 0.001 PHE A 432 TRP 0.007 0.001 TRP A 339 HIS 0.002 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 2140) covalent geometry : angle 0.46669 ( 2916) hydrogen bonds : bond 0.02953 ( 92) hydrogen bonds : angle 4.82382 ( 273) *********************** 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 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.051 Fit side-chains REVERT: A 296 ARG cc_start: 0.8358 (ttm170) cc_final: 0.8143 (ttm170) REVERT: A 316 LYS cc_start: 0.8301 (mmpt) cc_final: 0.8038 (mtpt) REVERT: A 410 GLN cc_start: 0.8845 (mt0) cc_final: 0.8489 (mt0) outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.6653 time to fit residues: 24.9561 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 : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- 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 = 0.136361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106211 restraints weight = 2418.608| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.70 r_work: 0.3112 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1969 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 : 0.504 5.416 2916 Z= 0.261 Chirality : 0.043 0.126 333 Planarity : 0.005 0.055 379 Dihedral : 4.326 21.376 294 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.75 % Allowed : 15.79 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.51), residues: 262 helix: 2.47 (0.58), residues: 76 sheet: 0.88 (0.61), residues: 70 loop : -0.57 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 380 TYR 0.009 0.002 TYR A 365 PHE 0.005 0.001 PHE A 432 TRP 0.010 0.001 TRP A 52 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2140) covalent geometry : angle 0.50353 ( 2916) hydrogen bonds : bond 0.03562 ( 92) hydrogen bonds : angle 4.90876 ( 273) *********************** 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 41 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.051 Fit side-chains REVERT: A 296 ARG cc_start: 0.8344 (ttm170) cc_final: 0.8124 (ttm170) REVERT: A 316 LYS cc_start: 0.8310 (mmpt) cc_final: 0.8047 (mtpt) REVERT: A 410 GLN cc_start: 0.8858 (mt0) cc_final: 0.8494 (mt0) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.5885 time to fit residues: 23.8867 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 : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 279 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.137752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107663 restraints weight = 2389.805| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.69 r_work: 0.3101 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2140 Z= 0.109 Angle : 0.492 5.370 2916 Z= 0.256 Chirality : 0.042 0.131 333 Planarity : 0.005 0.055 379 Dihedral : 4.202 20.834 294 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.51), residues: 262 helix: 2.58 (0.58), residues: 76 sheet: 0.94 (0.61), residues: 70 loop : -0.50 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 380 TYR 0.007 0.001 TYR A 365 PHE 0.006 0.001 PHE A 432 TRP 0.006 0.001 TRP A 52 HIS 0.001 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 2140) covalent geometry : angle 0.49225 ( 2916) hydrogen bonds : bond 0.03118 ( 92) hydrogen bonds : angle 4.81223 ( 273) *********************** 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 38 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.087 Fit side-chains REVERT: A 296 ARG cc_start: 0.8352 (ttm170) cc_final: 0.8140 (ttm170) REVERT: A 316 LYS cc_start: 0.8304 (mmpt) cc_final: 0.8049 (mtpt) REVERT: A 410 GLN cc_start: 0.8834 (mt0) cc_final: 0.8463 (mt0) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.8154 time to fit residues: 30.6021 Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 22 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.137388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107086 restraints weight = 2442.694| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.72 r_work: 0.3121 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2140 Z= 0.115 Angle : 0.494 5.372 2916 Z= 0.257 Chirality : 0.042 0.126 333 Planarity : 0.005 0.054 379 Dihedral : 4.220 20.891 294 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.51), residues: 262 helix: 2.59 (0.58), residues: 76 sheet: 0.89 (0.61), residues: 70 loop : -0.51 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 380 TYR 0.007 0.001 TYR A 365 PHE 0.006 0.001 PHE A 432 TRP 0.007 0.001 TRP A 52 HIS 0.001 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 2140) covalent geometry : angle 0.49388 ( 2916) hydrogen bonds : bond 0.03249 ( 92) hydrogen bonds : angle 4.83280 ( 273) ********************** 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 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.097 Fit side-chains REVERT: A 296 ARG cc_start: 0.8346 (ttm170) cc_final: 0.8131 (ttm170) REVERT: A 316 LYS cc_start: 0.8301 (mmpt) cc_final: 0.8052 (mtpt) REVERT: A 410 GLN cc_start: 0.8828 (mt0) cc_final: 0.8460 (mt0) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.8491 time to fit residues: 30.1511 Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106105 restraints weight = 2488.895| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.69 r_work: 0.3104 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2140 Z= 0.133 Angle : 0.519 5.478 2916 Z= 0.270 Chirality : 0.043 0.129 333 Planarity : 0.005 0.057 379 Dihedral : 4.345 21.397 294 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.29 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.51), residues: 262 helix: 2.51 (0.58), residues: 76 sheet: 0.82 (0.60), residues: 70 loop : -0.52 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 380 TYR 0.009 0.002 TYR A 365 PHE 0.005 0.001 PHE A 307 TRP 0.009 0.001 TRP A 52 HIS 0.001 0.000 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2140) covalent geometry : angle 0.51906 ( 2916) hydrogen bonds : bond 0.03547 ( 92) hydrogen bonds : angle 4.89951 ( 273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1350.78 seconds wall clock time: 23 minutes 52.80 seconds (1432.80 seconds total)