Starting phenix.real_space_refine on Wed Mar 5 17:37:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrr_18624/03_2025/8qrr_18624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrr_18624/03_2025/8qrr_18624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrr_18624/03_2025/8qrr_18624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrr_18624/03_2025/8qrr_18624.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrr_18624/03_2025/8qrr_18624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrr_18624/03_2025/8qrr_18624.cif" } resolution = 2.78 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= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 Na 3 4.78 5 C 2052 2.51 5 N 512 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3129 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3116 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 16, 'TRANS': 403} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 2.61, per 1000 atoms: 0.83 Number of scatterers: 3129 At special positions: 0 Unit cell: (60.192, 70.224, 75.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 Na 3 11.00 O 546 8.00 N 512 7.00 C 2052 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: 1.15 Conformation dependent library (CDL) restraints added in 431.8 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 85.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 52 through 75 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 82 through 103 removed outlier: 3.687A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.795A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 249 through 292 removed outlier: 4.530A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 302 through 319 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.731A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 383 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 426 removed outlier: 4.110A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.522A pdb=" N ALA B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.640A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 210 260 hydrogen bonds defined for protein. 780 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: 0.95 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 988 1.34 - 1.46: 426 1.46 - 1.57: 1742 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3181 Sorted by residual: bond pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.19e-01 bond pdb=" CG LEU B 112 " pdb=" CD1 LEU B 112 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.51e-01 bond pdb=" CG LEU B 107 " pdb=" CD1 LEU B 107 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.02e-01 bond pdb=" CG1 ILE B 104 " pdb=" CD1 ILE B 104 " ideal model delta sigma weight residual 1.513 1.490 0.023 3.90e-02 6.57e+02 3.35e-01 bond pdb=" CA VAL B 472 " pdb=" C VAL B 472 " ideal model delta sigma weight residual 1.523 1.516 0.007 1.27e-02 6.20e+03 3.31e-01 ... (remaining 3176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 4214 1.12 - 2.23: 80 2.23 - 3.35: 23 3.35 - 4.47: 8 4.47 - 5.58: 7 Bond angle restraints: 4332 Sorted by residual: angle pdb=" CB ARG B 301 " pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 111.30 116.88 -5.58 2.30e+00 1.89e-01 5.89e+00 angle pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " pdb=" NE ARG B 301 " ideal model delta sigma weight residual 112.00 117.10 -5.10 2.20e+00 2.07e-01 5.37e+00 angle pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " pdb=" CG2 VAL B 459 " ideal model delta sigma weight residual 110.40 114.29 -3.89 1.70e+00 3.46e-01 5.25e+00 angle pdb=" N ILE B 103 " pdb=" CA ILE B 103 " pdb=" C ILE B 103 " ideal model delta sigma weight residual 109.34 113.04 -3.70 2.08e+00 2.31e-01 3.16e+00 angle pdb=" N VAL B 459 " pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 112.16 110.10 2.06 1.30e+00 5.92e-01 2.51e+00 ... (remaining 4327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1669 17.95 - 35.89: 166 35.89 - 53.83: 28 53.83 - 71.78: 1 71.78 - 89.72: 3 Dihedral angle restraints: 1867 sinusoidal: 681 harmonic: 1186 Sorted by residual: dihedral pdb=" CA ASP B 294 " pdb=" CB ASP B 294 " pdb=" CG ASP B 294 " pdb=" OD1 ASP B 294 " ideal model delta sinusoidal sigma weight residual -30.00 -86.47 56.47 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " pdb=" CD GLU B 251 " pdb=" OE1 GLU B 251 " ideal model delta sinusoidal sigma weight residual 0.00 85.67 -85.67 1 3.00e+01 1.11e-03 9.86e+00 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -130.28 -49.72 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 1864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 468 0.059 - 0.118: 73 0.118 - 0.177: 1 0.177 - 0.235: 0 0.235 - 0.294: 1 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PHE B 91 " pdb=" N PHE B 91 " pdb=" C PHE B 91 " pdb=" CB PHE B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 540 not shown) Planarity restraints: 536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 474 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C GLY B 474 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY B 474 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP B 475 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 471 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASN B 471 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN B 471 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 472 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 469 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C VAL B 469 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 469 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 470 " -0.009 2.00e-02 2.50e+03 ... (remaining 533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 617 2.77 - 3.30: 3207 3.30 - 3.83: 5511 3.83 - 4.37: 6085 4.37 - 4.90: 11075 Nonbonded interactions: 26495 Sorted by model distance: nonbonded pdb=" OD1 ASP B 388 " pdb="NA NA B 603 " model vdw 2.234 2.470 nonbonded pdb=" O PHE B 135 " pdb="NA NA B 603 " model vdw 2.255 2.470 nonbonded pdb=" OG1 THR B 139 " pdb="NA NA B 603 " model vdw 2.278 2.470 nonbonded pdb=" OD1 ASN B 386 " pdb="NA NA B 603 " model vdw 2.288 2.470 nonbonded pdb=" OG1 THR B 138 " pdb="NA NA B 603 " model vdw 2.310 2.470 ... (remaining 26490 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: 0.840 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.540 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:14.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.174 Angle : 0.491 5.583 4332 Z= 0.255 Chirality : 0.039 0.294 543 Planarity : 0.005 0.055 536 Dihedral : 14.324 89.721 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.21 % Allowed : 18.48 % Favored : 80.30 % 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: 2.25 (0.43), residues: 414 helix: 1.96 (0.29), residues: 340 sheet: -1.40 (1.27), residues: 20 loop : -0.25 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 338 HIS 0.001 0.001 HIS B 452 PHE 0.008 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.014 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.326 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 1.0031 time to fit residues: 46.8380 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 410 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.129492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094474 restraints weight = 3645.211| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.96 r_work: 0.2954 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.206 Angle : 0.510 6.133 4332 Z= 0.255 Chirality : 0.039 0.199 543 Planarity : 0.004 0.030 536 Dihedral : 3.771 29.938 446 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.03 % Allowed : 17.27 % Favored : 79.70 % 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: 2.93 (0.43), residues: 414 helix: 2.43 (0.28), residues: 341 sheet: -1.37 (1.28), residues: 20 loop : 0.01 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.008 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.413 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.9463 time to fit residues: 50.1800 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093233 restraints weight = 3595.219| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.95 r_work: 0.2935 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3181 Z= 0.233 Angle : 0.508 5.235 4332 Z= 0.255 Chirality : 0.040 0.239 543 Planarity : 0.004 0.031 536 Dihedral : 3.250 13.437 441 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.55 % Allowed : 16.06 % Favored : 79.39 % 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: 2.85 (0.42), residues: 414 helix: 2.43 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.88 (0.70), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.002 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.012 0.001 TYR B 334 ARG 0.007 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.361 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 49 average time/residue: 1.0004 time to fit residues: 50.9128 Evaluate side-chains 41 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093483 restraints weight = 3701.471| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.96 r_work: 0.2940 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3181 Z= 0.215 Angle : 0.500 5.150 4332 Z= 0.251 Chirality : 0.040 0.261 543 Planarity : 0.004 0.031 536 Dihedral : 3.257 13.818 441 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 5.15 % Allowed : 15.15 % Favored : 79.70 % 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: 2.87 (0.42), residues: 414 helix: 2.45 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.91 (0.69), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 338 HIS 0.001 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.011 0.001 TYR B 334 ARG 0.009 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.336 Fit side-chains REVERT: B 288 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7485 (mptp) outliers start: 17 outliers final: 5 residues processed: 51 average time/residue: 0.8642 time to fit residues: 46.0574 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.129857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095058 restraints weight = 3653.139| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.97 r_work: 0.2963 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3181 Z= 0.187 Angle : 0.494 5.258 4332 Z= 0.246 Chirality : 0.039 0.272 543 Planarity : 0.004 0.032 536 Dihedral : 3.203 11.933 441 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.94 % Allowed : 16.06 % Favored : 80.00 % 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: 2.91 (0.42), residues: 414 helix: 2.50 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.97 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.011 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.357 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 48 average time/residue: 0.9161 time to fit residues: 45.7815 Evaluate side-chains 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.129511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094428 restraints weight = 3759.504| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.00 r_work: 0.2956 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3181 Z= 0.198 Angle : 0.500 5.880 4332 Z= 0.248 Chirality : 0.040 0.281 543 Planarity : 0.004 0.038 536 Dihedral : 3.208 12.405 441 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.85 % Allowed : 15.76 % Favored : 79.39 % 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: 2.91 (0.42), residues: 414 helix: 2.51 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.02 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.013 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.348 Fit side-chains REVERT: B 292 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6455 (mpt) outliers start: 16 outliers final: 5 residues processed: 49 average time/residue: 0.8315 time to fit residues: 42.5614 Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095342 restraints weight = 3631.226| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.98 r_work: 0.2969 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.193 Angle : 0.506 6.004 4332 Z= 0.250 Chirality : 0.040 0.294 543 Planarity : 0.004 0.041 536 Dihedral : 3.212 12.546 441 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.94 % Allowed : 16.36 % Favored : 79.70 % 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: 2.95 (0.42), residues: 414 helix: 2.54 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.05 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.013 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.385 Fit side-chains REVERT: B 292 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6503 (mpt) outliers start: 13 outliers final: 5 residues processed: 48 average time/residue: 0.9610 time to fit residues: 47.9499 Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093997 restraints weight = 3663.355| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.98 r_work: 0.2949 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3181 Z= 0.224 Angle : 0.522 6.059 4332 Z= 0.257 Chirality : 0.040 0.300 543 Planarity : 0.004 0.043 536 Dihedral : 3.231 12.845 441 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.73 % Allowed : 17.27 % Favored : 80.00 % 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: 2.92 (0.42), residues: 414 helix: 2.51 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.00 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.011 0.001 TYR B 334 ARG 0.014 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.366 Fit side-chains REVERT: B 292 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6462 (mpt) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.8940 time to fit residues: 41.9580 Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.093991 restraints weight = 3671.682| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.98 r_work: 0.2950 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3181 Z= 0.217 Angle : 0.521 6.243 4332 Z= 0.257 Chirality : 0.040 0.303 543 Planarity : 0.004 0.048 536 Dihedral : 3.251 12.455 441 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.73 % Allowed : 17.27 % Favored : 80.00 % 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: 2.92 (0.42), residues: 414 helix: 2.51 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.02 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.012 0.001 TYR B 334 ARG 0.014 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.358 Fit side-chains REVERT: B 288 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7488 (mptp) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.9172 time to fit residues: 43.0693 Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.0020 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.131026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096063 restraints weight = 3615.862| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.97 r_work: 0.2978 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.171 Angle : 0.508 6.511 4332 Z= 0.250 Chirality : 0.040 0.302 543 Planarity : 0.004 0.049 536 Dihedral : 3.223 12.392 441 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.21 % Allowed : 19.09 % Favored : 79.70 % 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: 2.99 (0.42), residues: 414 helix: 2.57 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.06 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.008 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.015 0.001 ARG B 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.360 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.9264 time to fit residues: 42.4589 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.0010 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.130517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.095352 restraints weight = 3678.714| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.00 r_work: 0.2972 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.190 Angle : 0.506 6.518 4332 Z= 0.248 Chirality : 0.038 0.136 543 Planarity : 0.004 0.050 536 Dihedral : 3.214 12.018 441 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.91 % Allowed : 19.09 % Favored : 80.00 % 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: 2.98 (0.42), residues: 414 helix: 2.56 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.02 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.015 0.001 ARG B 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.53 seconds wall clock time: 43 minutes 5.46 seconds (2585.46 seconds total)