Starting phenix.real_space_refine on Wed Mar 12 03:44:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6coy_7544/03_2025/6coy_7544.cif Found real_map, /net/cci-nas-00/data/ceres_data/6coy_7544/03_2025/6coy_7544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6coy_7544/03_2025/6coy_7544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6coy_7544/03_2025/6coy_7544.map" model { file = "/net/cci-nas-00/data/ceres_data/6coy_7544/03_2025/6coy_7544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6coy_7544/03_2025/6coy_7544.cif" } resolution = 3.36 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= 0.003 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 58 5.16 5 Cl 4 4.86 5 C 4776 2.51 5 N 1130 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7156 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3576 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 6.36, per 1000 atoms: 0.89 Number of scatterers: 7156 At special positions: 0 Unit cell: (110.21, 77.25, 76.22, 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) Cl 4 17.00 S 58 16.00 O 1188 8.00 N 1130 7.00 C 4776 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: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 78.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 116 through 152 Processing helix chain 'A' and resid 156 through 183 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.538A pdb=" N THR A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 299 through 323 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 379 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.707A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 439 through 450 removed outlier: 6.892A pdb=" N GLN A 445 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 475 Processing helix chain 'A' and resid 483 through 503 Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 541 through 551 Processing helix chain 'A' and resid 555 through 571 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'B' and resid 117 through 152 Processing helix chain 'B' and resid 156 through 183 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 231 through 250 Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.538A pdb=" N THR B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 299 through 323 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 347 through 379 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.707A pdb=" N LYS B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 439 through 450 removed outlier: 6.892A pdb=" N GLN B 445 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 475 Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'B' and resid 521 through 538 Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'B' and resid 555 through 571 Processing helix chain 'B' and resid 576 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA3, first strand: chain 'B' and resid 510 through 512 551 hydrogen bonds defined for protein. 1551 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: 2.01 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1096 1.31 - 1.43: 2014 1.43 - 1.56: 4140 1.56 - 1.68: 4 1.68 - 1.81: 98 Bond restraints: 7352 Sorted by residual: bond pdb=" CB ILE A 556 " pdb=" CG1 ILE A 556 " ideal model delta sigma weight residual 1.530 1.377 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CB ILE B 556 " pdb=" CG1 ILE B 556 " ideal model delta sigma weight residual 1.530 1.377 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CB HIS B 538 " pdb=" CG HIS B 538 " ideal model delta sigma weight residual 1.497 1.424 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CB HIS A 538 " pdb=" CG HIS A 538 " ideal model delta sigma weight residual 1.497 1.424 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CB ILE B 553 " pdb=" CG1 ILE B 553 " ideal model delta sigma weight residual 1.530 1.431 0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 7347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 9310 2.64 - 5.28: 636 5.28 - 7.91: 52 7.91 - 10.55: 6 10.55 - 13.19: 2 Bond angle restraints: 10006 Sorted by residual: angle pdb=" C THR B 281 " pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 119.24 127.81 -8.57 1.04e+00 9.25e-01 6.80e+01 angle pdb=" C THR A 281 " pdb=" N PRO A 282 " pdb=" CA PRO A 282 " ideal model delta sigma weight residual 119.24 127.81 -8.57 1.04e+00 9.25e-01 6.80e+01 angle pdb=" C LEU A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.47 128.00 -8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C LEU B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.47 128.00 -8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C PHE B 341 " pdb=" N PRO B 342 " pdb=" CA PRO B 342 " ideal model delta sigma weight residual 119.56 125.93 -6.37 1.01e+00 9.80e-01 3.97e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4126 17.23 - 34.46: 86 34.46 - 51.69: 18 51.69 - 68.91: 18 68.91 - 86.14: 6 Dihedral angle restraints: 4254 sinusoidal: 1592 harmonic: 2662 Sorted by residual: dihedral pdb=" CA THR B 432 " pdb=" C THR B 432 " pdb=" N TRP B 433 " pdb=" CA TRP B 433 " ideal model delta harmonic sigma weight residual 180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA THR A 432 " pdb=" C THR A 432 " pdb=" N TRP A 433 " pdb=" CA TRP A 433 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" C TYR B 393 " pdb=" N TYR B 393 " pdb=" CA TYR B 393 " pdb=" CB TYR B 393 " ideal model delta harmonic sigma weight residual -122.60 -130.59 7.99 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 4251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 684 0.069 - 0.139: 342 0.139 - 0.208: 102 0.208 - 0.278: 34 0.278 - 0.347: 8 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO B 407 " pdb=" N PRO B 407 " pdb=" C PRO B 407 " pdb=" CB PRO B 407 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO B 558 " pdb=" N PRO B 558 " pdb=" C PRO B 558 " pdb=" CB PRO B 558 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1167 not shown) Planarity restraints: 1224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 590 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO B 591 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 590 " 0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO A 591 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 485 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 486 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 486 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 486 " 0.056 5.00e-02 4.00e+02 ... (remaining 1221 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1662 2.77 - 3.31: 7383 3.31 - 3.84: 12334 3.84 - 4.37: 14469 4.37 - 4.90: 24411 Nonbonded interactions: 60259 Sorted by model distance: nonbonded pdb=" N GLN A 185 " pdb=" OE1 GLN A 185 " model vdw 2.242 3.120 nonbonded pdb=" N GLN B 185 " pdb=" OE1 GLN B 185 " model vdw 2.242 3.120 nonbonded pdb=" CB GLU A 291 " pdb=" OE1 GLU A 291 " model vdw 2.449 2.752 nonbonded pdb=" CB GLU B 291 " pdb=" OE1 GLU B 291 " model vdw 2.449 2.752 nonbonded pdb=" OE1 GLU B 291 " pdb=" OG1 THR B 539 " model vdw 2.501 3.040 ... (remaining 60254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.280 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.880 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:2.800 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: 0.8256 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 : 0.020 0.153 7352 Z= 1.323 Angle : 1.425 13.192 10006 Z= 0.978 Chirality : 0.091 0.347 1170 Planarity : 0.014 0.150 1224 Dihedral : 10.542 86.142 2546 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 2.82 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 (0.25), residues: 922 helix: 0.29 (0.18), residues: 668 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 322 HIS 0.007 0.002 HIS B 436 PHE 0.029 0.005 PHE A 547 TYR 0.044 0.010 TYR B 296 ARG 0.006 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1330 time to fit residues: 24.2058 Evaluate side-chains 82 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 436 HIS A 538 HIS B 369 HIS B 436 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.103590 restraints weight = 8490.010| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.73 r_work: 0.2947 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7352 Z= 0.262 Angle : 0.614 6.437 10006 Z= 0.330 Chirality : 0.043 0.149 1170 Planarity : 0.008 0.072 1224 Dihedral : 4.176 15.137 978 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.57 % Allowed : 5.64 % Favored : 92.78 % 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: 1.95 (0.28), residues: 922 helix: 1.99 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -0.65 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.003 0.001 HIS A 451 PHE 0.030 0.002 PHE A 547 TYR 0.011 0.002 TYR B 589 ARG 0.002 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8284 (t0) cc_final: 0.7836 (t0) REVERT: A 346 LYS cc_start: 0.8169 (mttt) cc_final: 0.7583 (mptt) REVERT: A 466 MET cc_start: 0.7434 (mmt) cc_final: 0.7178 (mmt) REVERT: A 583 GLN cc_start: 0.6887 (mt0) cc_final: 0.6663 (tt0) REVERT: B 325 ASP cc_start: 0.8292 (t0) cc_final: 0.7845 (t0) REVERT: B 346 LYS cc_start: 0.8165 (mttt) cc_final: 0.7584 (mptt) REVERT: B 466 MET cc_start: 0.7455 (mmt) cc_final: 0.7197 (mmt) REVERT: B 583 GLN cc_start: 0.6911 (mt0) cc_final: 0.6681 (tt0) outliers start: 12 outliers final: 8 residues processed: 136 average time/residue: 0.1464 time to fit residues: 28.7546 Evaluate side-chains 116 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.119564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.102588 restraints weight = 8681.301| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.83 r_work: 0.2935 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7352 Z= 0.236 Angle : 0.542 6.232 10006 Z= 0.289 Chirality : 0.042 0.143 1170 Planarity : 0.006 0.064 1224 Dihedral : 3.852 13.896 978 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.36 % Allowed : 8.01 % Favored : 89.63 % 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: 2.58 (0.28), residues: 922 helix: 2.54 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.59 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.002 0.001 HIS A 451 PHE 0.030 0.002 PHE B 547 TYR 0.008 0.001 TYR A 146 ARG 0.003 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 THR cc_start: 0.8975 (m) cc_final: 0.8603 (t) REVERT: A 325 ASP cc_start: 0.8522 (t0) cc_final: 0.8096 (t0) REVERT: A 346 LYS cc_start: 0.8090 (mttt) cc_final: 0.7544 (mptt) REVERT: A 466 MET cc_start: 0.7457 (mmt) cc_final: 0.7185 (mmt) REVERT: A 583 GLN cc_start: 0.7183 (mt0) cc_final: 0.6893 (tt0) REVERT: B 295 THR cc_start: 0.8963 (m) cc_final: 0.8592 (t) REVERT: B 325 ASP cc_start: 0.8519 (t0) cc_final: 0.8081 (t0) REVERT: B 346 LYS cc_start: 0.8088 (mttt) cc_final: 0.7543 (mptt) REVERT: B 466 MET cc_start: 0.7466 (mmt) cc_final: 0.7194 (mmt) REVERT: B 583 GLN cc_start: 0.7180 (mt0) cc_final: 0.6892 (tt0) outliers start: 18 outliers final: 12 residues processed: 120 average time/residue: 0.1647 time to fit residues: 27.9585 Evaluate side-chains 112 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 0.2980 chunk 67 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 29 optimal weight: 0.0020 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.121929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.104944 restraints weight = 8551.831| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.83 r_work: 0.2967 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7352 Z= 0.182 Angle : 0.510 6.445 10006 Z= 0.266 Chirality : 0.040 0.141 1170 Planarity : 0.006 0.062 1224 Dihedral : 3.735 13.651 978 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.84 % Allowed : 9.84 % Favored : 88.32 % 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: 2.89 (0.28), residues: 922 helix: 2.79 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.54 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.002 0.001 HIS B 451 PHE 0.028 0.001 PHE B 547 TYR 0.007 0.001 TYR A 137 ARG 0.001 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LYS cc_start: 0.7556 (ttpt) cc_final: 0.7060 (ptmm) REVERT: A 295 THR cc_start: 0.8902 (m) cc_final: 0.8581 (t) REVERT: A 325 ASP cc_start: 0.8462 (t0) cc_final: 0.8048 (t0) REVERT: A 346 LYS cc_start: 0.7993 (mttt) cc_final: 0.7540 (mptt) REVERT: A 583 GLN cc_start: 0.7197 (mt0) cc_final: 0.6890 (tt0) REVERT: B 204 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7064 (ptmm) REVERT: B 295 THR cc_start: 0.8898 (m) cc_final: 0.8579 (t) REVERT: B 325 ASP cc_start: 0.8475 (t0) cc_final: 0.8066 (t0) REVERT: B 346 LYS cc_start: 0.7986 (mttt) cc_final: 0.7525 (mptt) REVERT: B 583 GLN cc_start: 0.7184 (mt0) cc_final: 0.6876 (tt0) outliers start: 14 outliers final: 12 residues processed: 118 average time/residue: 0.1452 time to fit residues: 25.2482 Evaluate side-chains 128 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.121387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.104368 restraints weight = 8530.277| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.82 r_work: 0.2957 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7352 Z= 0.201 Angle : 0.505 5.681 10006 Z= 0.264 Chirality : 0.041 0.142 1170 Planarity : 0.006 0.058 1224 Dihedral : 3.618 14.378 978 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.62 % Allowed : 9.84 % Favored : 87.53 % 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: 2.90 (0.28), residues: 922 helix: 2.81 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.61 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.002 0.001 HIS A 451 PHE 0.028 0.001 PHE A 547 TYR 0.007 0.001 TYR B 137 ARG 0.002 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 THR cc_start: 0.8973 (m) cc_final: 0.8629 (t) REVERT: A 325 ASP cc_start: 0.8629 (t0) cc_final: 0.8192 (t0) REVERT: A 346 LYS cc_start: 0.8001 (mttt) cc_final: 0.7537 (mptt) REVERT: A 410 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7541 (ttt) REVERT: A 583 GLN cc_start: 0.7213 (mt0) cc_final: 0.6877 (tt0) REVERT: B 295 THR cc_start: 0.8966 (m) cc_final: 0.8620 (t) REVERT: B 325 ASP cc_start: 0.8629 (t0) cc_final: 0.8199 (t0) REVERT: B 346 LYS cc_start: 0.8011 (mttt) cc_final: 0.7544 (mptt) REVERT: B 410 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7554 (ttt) REVERT: B 583 GLN cc_start: 0.7210 (mt0) cc_final: 0.6871 (tt0) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.1721 time to fit residues: 30.6786 Evaluate side-chains 131 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 0.0170 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.119596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.102425 restraints weight = 8677.307| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.83 r_work: 0.2932 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7352 Z= 0.219 Angle : 0.510 5.640 10006 Z= 0.266 Chirality : 0.041 0.140 1170 Planarity : 0.006 0.060 1224 Dihedral : 3.592 13.934 978 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.41 % Allowed : 9.84 % Favored : 86.75 % 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: 2.86 (0.28), residues: 922 helix: 2.78 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.62 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.002 0.001 HIS A 451 PHE 0.028 0.001 PHE A 547 TYR 0.007 0.001 TYR B 137 ARG 0.001 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7572 (t80) REVERT: A 325 ASP cc_start: 0.8560 (t0) cc_final: 0.8127 (t0) REVERT: A 346 LYS cc_start: 0.8020 (mttt) cc_final: 0.7566 (mptt) REVERT: A 410 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7483 (ttt) REVERT: A 583 GLN cc_start: 0.7219 (mt0) cc_final: 0.6864 (tt0) REVERT: B 235 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7581 (t80) REVERT: B 325 ASP cc_start: 0.8560 (t0) cc_final: 0.8129 (t0) REVERT: B 346 LYS cc_start: 0.8019 (mttt) cc_final: 0.7565 (mptt) REVERT: B 410 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7483 (ttt) REVERT: B 583 GLN cc_start: 0.7213 (mt0) cc_final: 0.6859 (tt0) outliers start: 26 outliers final: 22 residues processed: 130 average time/residue: 0.1420 time to fit residues: 27.3290 Evaluate side-chains 134 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 547 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3240 r_free = 0.3240 target = 0.120205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.102896 restraints weight = 8595.355| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.84 r_work: 0.2935 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7352 Z= 0.209 Angle : 0.513 6.008 10006 Z= 0.264 Chirality : 0.041 0.142 1170 Planarity : 0.006 0.056 1224 Dihedral : 3.550 13.987 978 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.15 % Allowed : 10.37 % Favored : 86.48 % 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: 2.94 (0.28), residues: 922 helix: 2.83 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.55 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.002 0.001 HIS A 451 PHE 0.028 0.001 PHE B 547 TYR 0.007 0.001 TYR A 137 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7646 (t80) REVERT: A 295 THR cc_start: 0.8998 (m) cc_final: 0.8634 (t) REVERT: A 325 ASP cc_start: 0.8653 (t0) cc_final: 0.8196 (t0) REVERT: A 410 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7525 (ttt) REVERT: A 583 GLN cc_start: 0.7325 (mt0) cc_final: 0.6947 (tt0) REVERT: B 235 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7657 (t80) REVERT: B 295 THR cc_start: 0.8998 (m) cc_final: 0.8632 (t) REVERT: B 325 ASP cc_start: 0.8673 (t0) cc_final: 0.8221 (t0) REVERT: B 410 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7539 (ttt) REVERT: B 583 GLN cc_start: 0.7306 (mt0) cc_final: 0.6928 (tt0) outliers start: 24 outliers final: 18 residues processed: 122 average time/residue: 0.1348 time to fit residues: 24.6079 Evaluate side-chains 132 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 547 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.117853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.100391 restraints weight = 8669.207| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.88 r_work: 0.2900 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7352 Z= 0.273 Angle : 0.545 6.470 10006 Z= 0.283 Chirality : 0.042 0.140 1170 Planarity : 0.006 0.058 1224 Dihedral : 3.604 13.561 978 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.81 % Allowed : 9.97 % Favored : 86.22 % 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: 2.71 (0.28), residues: 922 helix: 2.68 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.002 0.001 HIS A 451 PHE 0.029 0.002 PHE A 547 TYR 0.008 0.001 TYR B 137 ARG 0.002 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 325 ASP cc_start: 0.8653 (t0) cc_final: 0.8156 (t0) REVERT: A 410 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7601 (ttt) REVERT: A 583 GLN cc_start: 0.7347 (mt0) cc_final: 0.6950 (tt0) REVERT: B 235 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7736 (t80) REVERT: B 325 ASP cc_start: 0.8673 (t0) cc_final: 0.8182 (t0) REVERT: B 410 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7605 (ttt) REVERT: B 583 GLN cc_start: 0.7353 (mt0) cc_final: 0.6950 (tt0) outliers start: 29 outliers final: 25 residues processed: 126 average time/residue: 0.1329 time to fit residues: 25.4332 Evaluate side-chains 134 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.117935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100743 restraints weight = 8715.354| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.84 r_work: 0.2906 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7352 Z= 0.257 Angle : 0.542 7.225 10006 Z= 0.281 Chirality : 0.042 0.141 1170 Planarity : 0.006 0.057 1224 Dihedral : 3.608 13.505 978 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.67 % Allowed : 9.97 % Favored : 86.35 % 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: 2.71 (0.28), residues: 922 helix: 2.68 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.002 0.001 HIS B 451 PHE 0.029 0.002 PHE B 547 TYR 0.008 0.001 TYR A 137 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8334 (tp40) REVERT: A 235 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7580 (t80) REVERT: A 295 THR cc_start: 0.8986 (m) cc_final: 0.8631 (t) REVERT: A 325 ASP cc_start: 0.8682 (t0) cc_final: 0.8176 (t0) REVERT: A 410 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7485 (ttt) REVERT: B 152 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8330 (tp40) REVERT: B 235 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 295 THR cc_start: 0.8986 (m) cc_final: 0.8631 (t) REVERT: B 325 ASP cc_start: 0.8698 (t0) cc_final: 0.8199 (t0) REVERT: B 410 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7493 (ttt) outliers start: 28 outliers final: 22 residues processed: 122 average time/residue: 0.1560 time to fit residues: 29.0679 Evaluate side-chains 130 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.0370 chunk 33 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN B 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.121794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.104180 restraints weight = 8640.952| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.90 r_work: 0.2954 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7352 Z= 0.179 Angle : 0.508 7.758 10006 Z= 0.261 Chirality : 0.040 0.141 1170 Planarity : 0.005 0.057 1224 Dihedral : 3.523 14.289 978 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.76 % Allowed : 11.29 % 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: 3.00 (0.28), residues: 922 helix: 2.88 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.53 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 469 HIS 0.002 0.001 HIS A 451 PHE 0.027 0.001 PHE B 547 TYR 0.007 0.001 TYR B 137 ARG 0.002 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8307 (tp40) REVERT: A 235 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7565 (t80) REVERT: A 295 THR cc_start: 0.8960 (m) cc_final: 0.8660 (t) REVERT: A 325 ASP cc_start: 0.8690 (t0) cc_final: 0.8173 (t0) REVERT: B 152 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8320 (tp40) REVERT: B 235 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7580 (t80) REVERT: B 295 THR cc_start: 0.8960 (m) cc_final: 0.8652 (t) REVERT: B 325 ASP cc_start: 0.8698 (t0) cc_final: 0.8188 (t0) outliers start: 21 outliers final: 17 residues processed: 120 average time/residue: 0.1328 time to fit residues: 24.1021 Evaluate side-chains 123 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN B 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.119224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.101937 restraints weight = 8649.155| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.84 r_work: 0.2925 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7352 Z= 0.239 Angle : 0.529 7.897 10006 Z= 0.274 Chirality : 0.042 0.138 1170 Planarity : 0.006 0.056 1224 Dihedral : 3.526 14.157 978 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.89 % Allowed : 11.29 % Favored : 85.83 % 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 (0.28), residues: 922 helix: 2.78 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.63 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.002 0.001 HIS A 451 PHE 0.028 0.001 PHE A 547 TYR 0.007 0.001 TYR A 137 ARG 0.002 0.000 ARG B 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3260.68 seconds wall clock time: 57 minutes 6.78 seconds (3426.78 seconds total)