Starting phenix.real_space_refine on Fri May 9 13:27:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bje_44632/05_2025/9bje_44632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bje_44632/05_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_44632/05_2025/9bje_44632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bje_44632/05_2025/9bje_44632.map" model { file = "/net/cci-nas-00/data/ceres_data/9bje_44632/05_2025/9bje_44632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bje_44632/05_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-5687/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: 3.33, per 1000 atoms: 1.59 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: 0.48 Conformation dependent library (CDL) restraints added in 265.9 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: 0.29 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: 0.56 Time building geometry restraints manager: 0.58 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.700 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.520 ------------------------------------------------------------------------------- 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 : 0.253 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 1.3605 time to fit residues: 54.1476 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 : 0.227 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- 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 = 0.139541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109785 restraints weight = 2428.635| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.70 r_work: 0.3165 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1167 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 : 0.502 5.445 2916 Z= 0.261 Chirality : 0.043 0.126 333 Planarity : 0.005 0.049 379 Dihedral : 4.237 19.860 294 Min Nonbonded Distance : 2.621 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: 0.80 (0.51), residues: 262 helix: 1.85 (0.59), residues: 77 sheet: 1.09 (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 307 TYR 0.010 0.001 TYR A 60 ARG 0.003 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 92) hydrogen bonds : angle 5.07705 ( 273) covalent geometry : bond 0.00252 ( 2140) covalent geometry : angle 0.50203 ( 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 : 0.229 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 1.5255 time to fit residues: 55.9105 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 ------------------------------------------------------------------------------- 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: 0.5980 chunk 24 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.137169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107076 restraints weight = 2438.640| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.72 r_work: 0.3123 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1409 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= 0.141 Angle : 0.507 5.485 2916 Z= 0.264 Chirality : 0.043 0.128 333 Planarity : 0.005 0.055 379 Dihedral : 4.362 20.785 294 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 0.89 (0.51), residues: 262 helix: 1.97 (0.59), residues: 77 sheet: 1.00 (0.64), residues: 65 loop : -0.55 (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 0.010 0.002 TYR A 60 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 92) hydrogen bonds : angle 5.05475 ( 273) covalent geometry : bond 0.00334 ( 2140) covalent geometry : angle 0.50670 ( 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 : 0.255 Fit side-chains REVERT: A 301 MET cc_start: 0.9038 (mmt) cc_final: 0.8741 (mmt) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 1.4095 time to fit residues: 48.8768 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET 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: 2.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.137010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107124 restraints weight = 2376.052| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.68 r_work: 0.3104 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1640 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= 0.122 Angle : 0.482 5.411 2916 Z= 0.252 Chirality : 0.043 0.126 333 Planarity : 0.005 0.056 379 Dihedral : 4.343 20.917 294 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.32 % Allowed : 12.72 % Favored : 85.96 % 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: 1.89 (0.58), residues: 79 sheet: 0.88 (0.63), residues: 65 loop : -0.48 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 52 HIS 0.002 0.001 HIS A 311 PHE 0.006 0.002 PHE A 307 TYR 0.009 0.001 TYR A 60 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 92) hydrogen bonds : angle 4.93153 ( 273) covalent geometry : bond 0.00287 ( 2140) covalent geometry : angle 0.48238 ( 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: 3 poor density : 33 time to evaluate : 0.224 Fit side-chains REVERT: A 410 GLN cc_start: 0.8830 (mt0) cc_final: 0.8485 (mt0) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 1.5531 time to fit residues: 53.8046 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 : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.137831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107838 restraints weight = 2426.194| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.71 r_work: 0.3117 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.003 0.019 2140 Z= 0.110 Angle : 0.470 5.390 2916 Z= 0.244 Chirality : 0.042 0.126 333 Planarity : 0.005 0.055 379 Dihedral : 4.241 20.699 294 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.32 % Allowed : 15.35 % Favored : 83.33 % 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: 1.00 (0.51), residues: 262 helix: 2.02 (0.58), residues: 79 sheet: 0.87 (0.61), residues: 70 loop : -0.42 (0.57), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 339 HIS 0.001 0.000 HIS A 416 PHE 0.006 0.001 PHE A 432 TYR 0.007 0.001 TYR A 365 ARG 0.003 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 92) hydrogen bonds : angle 4.87287 ( 273) covalent geometry : bond 0.00257 ( 2140) covalent geometry : angle 0.47019 ( 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: 3 poor density : 32 time to evaluate : 0.250 Fit side-chains REVERT: A 316 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8070 (mmpt) REVERT: A 410 GLN cc_start: 0.8816 (mt0) cc_final: 0.8465 (mt0) outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 1.5498 time to fit residues: 53.7010 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 : 0.192 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.136644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106403 restraints weight = 2414.729| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.71 r_work: 0.3115 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1848 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= 0.132 Angle : 0.494 5.395 2916 Z= 0.258 Chirality : 0.043 0.126 333 Planarity : 0.005 0.056 379 Dihedral : 4.338 21.134 294 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.53 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 (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: 2.32 (0.58), residues: 76 sheet: 0.85 (0.63), residues: 65 loop : -0.46 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 365 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 92) hydrogen bonds : angle 4.92382 ( 273) covalent geometry : bond 0.00315 ( 2140) covalent geometry : angle 0.49420 ( 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 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.248 Fit side-chains REVERT: A 410 GLN cc_start: 0.8817 (mt0) cc_final: 0.8451 (mt0) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 1.4278 time to fit residues: 50.9557 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.134895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104419 restraints weight = 2425.401| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.72 r_work: 0.3081 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.005 0.032 2140 Z= 0.185 Angle : 0.545 5.568 2916 Z= 0.285 Chirality : 0.045 0.129 333 Planarity : 0.006 0.058 379 Dihedral : 4.604 22.135 294 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.19 % Allowed : 15.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.50), residues: 262 helix: 2.00 (0.57), residues: 77 sheet: 0.92 (0.60), residues: 68 loop : -0.62 (0.55), residues: 117 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 0.006 0.002 PHE A 307 TYR 0.012 0.002 TYR A 365 ARG 0.006 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 92) hydrogen bonds : angle 5.09159 ( 273) covalent geometry : bond 0.00452 ( 2140) covalent geometry : angle 0.54520 ( 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 41 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.231 Fit side-chains REVERT: A 283 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7356 (tp30) REVERT: A 410 GLN cc_start: 0.8873 (mt0) cc_final: 0.8521 (mt0) outliers start: 5 outliers final: 1 residues processed: 38 average time/residue: 1.2884 time to fit residues: 49.9926 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 : 0.247 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.138163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107878 restraints weight = 2456.222| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.73 r_work: 0.3134 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1904 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= 0.101 Angle : 0.478 5.368 2916 Z= 0.249 Chirality : 0.042 0.121 333 Planarity : 0.005 0.056 379 Dihedral : 4.218 20.659 294 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.51), residues: 262 helix: 2.40 (0.57), residues: 76 sheet: 0.88 (0.61), residues: 70 loop : -0.56 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 339 HIS 0.001 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 0.03068 ( 92) hydrogen bonds : angle 4.82702 ( 273) covalent geometry : bond 0.00234 ( 2140) covalent geometry : angle 0.47849 ( 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 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.250 Fit side-chains REVERT: A 316 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7950 (mtpt) REVERT: A 410 GLN cc_start: 0.8831 (mt0) cc_final: 0.8484 (mt0) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 1.4572 time to fit residues: 50.5517 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.135852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105322 restraints weight = 2463.766| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.72 r_work: 0.3099 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.004 0.029 2140 Z= 0.150 Angle : 0.529 5.467 2916 Z= 0.276 Chirality : 0.044 0.127 333 Planarity : 0.005 0.056 379 Dihedral : 4.417 21.525 294 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.58 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: 0.98 (0.51), residues: 262 helix: 2.31 (0.57), residues: 76 sheet: 0.79 (0.60), residues: 70 loop : -0.56 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 52 HIS 0.002 0.000 HIS A 311 PHE 0.005 0.002 PHE A 432 TYR 0.011 0.002 TYR A 365 ARG 0.003 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 92) hydrogen bonds : angle 4.93894 ( 273) covalent geometry : bond 0.00363 ( 2140) covalent geometry : angle 0.52858 ( 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 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.256 Fit side-chains REVERT: A 316 LYS cc_start: 0.8251 (mmpt) cc_final: 0.7948 (mtpt) REVERT: A 410 GLN cc_start: 0.8829 (mt0) cc_final: 0.8467 (mt0) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 1.4201 time to fit residues: 50.6898 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 : 0.231 ------------------------------------------------------------------------------- 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 25 optimal weight: 8.9990 chunk 18 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.137319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106882 restraints weight = 2405.256| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.71 r_work: 0.3118 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2140 Z= 0.118 Angle : 0.501 5.436 2916 Z= 0.261 Chirality : 0.043 0.124 333 Planarity : 0.005 0.056 379 Dihedral : 4.302 20.988 294 Min Nonbonded Distance : 2.549 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: 1.05 (0.51), residues: 262 helix: 2.48 (0.57), residues: 76 sheet: 0.84 (0.60), residues: 70 loop : -0.62 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 52 HIS 0.001 0.000 HIS A 416 PHE 0.006 0.001 PHE A 432 TYR 0.007 0.001 TYR A 365 ARG 0.002 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 92) hydrogen bonds : angle 4.85709 ( 273) covalent geometry : bond 0.00281 ( 2140) covalent geometry : angle 0.50130 ( 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 : 0.253 Fit side-chains REVERT: A 410 GLN cc_start: 0.8836 (mt0) cc_final: 0.8476 (mt0) outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 1.4769 time to fit residues: 49.7169 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 : 0.321 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 3 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3585 r_free = 0.3585 target = 0.135549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105430 restraints weight = 2461.043| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.66 r_work: 0.3099 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2140 Z= 0.164 Angle : 0.544 5.502 2916 Z= 0.284 Chirality : 0.044 0.128 333 Planarity : 0.005 0.057 379 Dihedral : 4.506 21.872 294 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.44 % Allowed : 17.54 % 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: 0.92 (0.50), residues: 262 helix: 2.32 (0.57), residues: 76 sheet: 0.72 (0.59), residues: 70 loop : -0.63 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 52 HIS 0.002 0.001 HIS A 311 PHE 0.005 0.002 PHE A 344 TYR 0.011 0.002 TYR A 365 ARG 0.003 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 92) hydrogen bonds : angle 5.02102 ( 273) covalent geometry : bond 0.00401 ( 2140) covalent geometry : angle 0.54431 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.23 seconds wall clock time: 44 minutes 19.31 seconds (2659.31 seconds total)