Starting phenix.real_space_refine on Wed Feb 12 04:04:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6coy_7544/02_2025/6coy_7544.cif Found real_map, /net/cci-nas-00/data/ceres_data/6coy_7544/02_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_7544/02_2025/6coy_7544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6coy_7544/02_2025/6coy_7544.map" model { file = "/net/cci-nas-00/data/ceres_data/6coy_7544/02_2025/6coy_7544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6coy_7544/02_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-5592/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: 6.62, per 1000 atoms: 0.93 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: 1.99 Conformation dependent library (CDL) restraints added in 1.0 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: 0.66 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: 2.00 Time building geometry restraints manager: 2.28 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: 0.03 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: 1.810 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- 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 : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1415 time to fit residues: 25.6133 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 : 0.684 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.119951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.103603 restraints weight = 8489.782| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.73 r_work: 0.2947 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2074 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= 0.261 Angle : 0.614 6.443 10006 Z= 0.330 Chirality : 0.043 0.149 1170 Planarity : 0.008 0.072 1224 Dihedral : 4.178 15.153 978 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 : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8284 (t0) cc_final: 0.7833 (t0) REVERT: A 346 LYS cc_start: 0.8172 (mttt) cc_final: 0.7586 (mptt) REVERT: A 466 MET cc_start: 0.7450 (mmt) cc_final: 0.7192 (mmt) REVERT: A 583 GLN cc_start: 0.6893 (mt0) cc_final: 0.6668 (tt0) REVERT: B 325 ASP cc_start: 0.8292 (t0) cc_final: 0.7844 (t0) REVERT: B 346 LYS cc_start: 0.8168 (mttt) cc_final: 0.7587 (mptt) REVERT: B 466 MET cc_start: 0.7466 (mmt) cc_final: 0.7207 (mmt) REVERT: B 583 GLN cc_start: 0.6917 (mt0) cc_final: 0.6686 (tt0) outliers start: 12 outliers final: 8 residues processed: 136 average time/residue: 0.1538 time to fit residues: 30.2967 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 : 0.835 ------------------------------------------------------------------------------- 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: 0.7980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.119143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102174 restraints weight = 8693.886| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.83 r_work: 0.2928 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2597 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= 0.245 Angle : 0.546 5.824 10006 Z= 0.292 Chirality : 0.042 0.145 1170 Planarity : 0.006 0.065 1224 Dihedral : 3.852 13.218 978 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.88 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: 2.55 (0.28), residues: 922 helix: 2.52 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.61 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.003 0.001 HIS B 451 PHE 0.030 0.002 PHE B 547 TYR 0.008 0.001 TYR A 146 ARG 0.002 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 124 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 THR cc_start: 0.8971 (m) cc_final: 0.8599 (t) REVERT: A 325 ASP cc_start: 0.8529 (t0) cc_final: 0.8098 (t0) REVERT: A 346 LYS cc_start: 0.8083 (mttt) cc_final: 0.7527 (mptt) REVERT: A 466 MET cc_start: 0.7454 (mmt) cc_final: 0.7187 (mmt) REVERT: A 583 GLN cc_start: 0.7183 (mt0) cc_final: 0.6889 (tt0) REVERT: B 295 THR cc_start: 0.8962 (m) cc_final: 0.8589 (t) REVERT: B 325 ASP cc_start: 0.8522 (t0) cc_final: 0.8079 (t0) REVERT: B 346 LYS cc_start: 0.8084 (mttt) cc_final: 0.7531 (mptt) REVERT: B 466 MET cc_start: 0.7468 (mmt) cc_final: 0.7200 (mmt) REVERT: B 583 GLN cc_start: 0.7181 (mt0) cc_final: 0.6888 (tt0) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.1486 time to fit residues: 25.5630 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 : 0.782 ------------------------------------------------------------------------------- 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: 0.0870 chunk 67 optimal weight: 0.0670 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.122169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.105345 restraints weight = 8510.784| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.81 r_work: 0.2971 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7352 Z= 0.178 Angle : 0.505 5.926 10006 Z= 0.264 Chirality : 0.040 0.141 1170 Planarity : 0.006 0.063 1224 Dihedral : 3.740 15.031 978 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.84 % Allowed : 9.58 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.28), residues: 922 helix: 2.81 (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 0.000 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 B 377 *********************** 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 122 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LYS cc_start: 0.7526 (ttpt) cc_final: 0.7036 (ptmm) REVERT: A 325 ASP cc_start: 0.8444 (t0) cc_final: 0.8029 (t0) REVERT: A 346 LYS cc_start: 0.7988 (mttt) cc_final: 0.7530 (mptt) REVERT: A 583 GLN cc_start: 0.7170 (mt0) cc_final: 0.6862 (tt0) REVERT: B 204 LYS cc_start: 0.7523 (ttpt) cc_final: 0.7033 (ptmm) REVERT: B 325 ASP cc_start: 0.8454 (t0) cc_final: 0.8045 (t0) REVERT: B 346 LYS cc_start: 0.7971 (mttt) cc_final: 0.7511 (mptt) REVERT: B 583 GLN cc_start: 0.7159 (mt0) cc_final: 0.6851 (tt0) outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.1486 time to fit residues: 25.4402 Evaluate side-chains 124 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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: 0.4980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.119310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.102272 restraints weight = 8612.573| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.83 r_work: 0.2926 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3005 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= 0.243 Angle : 0.524 5.648 10006 Z= 0.275 Chirality : 0.041 0.141 1170 Planarity : 0.006 0.059 1224 Dihedral : 3.653 13.943 978 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.28 % Allowed : 9.19 % 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: 2.79 (0.28), residues: 922 helix: 2.74 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.68 (0.40), residues: 256 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 0.028 0.002 PHE B 547 TYR 0.009 0.001 TYR B 146 ARG 0.002 0.000 ARG B 377 *********************** 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 135 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 THR cc_start: 0.8969 (m) cc_final: 0.8637 (t) REVERT: A 325 ASP cc_start: 0.8566 (t0) cc_final: 0.8124 (t0) REVERT: A 346 LYS cc_start: 0.8026 (mttt) cc_final: 0.7601 (mptt) REVERT: A 410 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7586 (ttt) REVERT: A 583 GLN cc_start: 0.7237 (mt0) cc_final: 0.6881 (tt0) REVERT: B 295 THR cc_start: 0.8967 (m) cc_final: 0.8634 (t) REVERT: B 325 ASP cc_start: 0.8560 (t0) cc_final: 0.8128 (t0) REVERT: B 346 LYS cc_start: 0.8025 (mttt) cc_final: 0.7600 (mptt) REVERT: B 410 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7595 (ttt) REVERT: B 583 GLN cc_start: 0.7230 (mt0) cc_final: 0.6870 (tt0) outliers start: 25 outliers final: 21 residues processed: 122 average time/residue: 0.1603 time to fit residues: 27.9229 Evaluate side-chains 131 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 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 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 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 477 MET Chi-restraints excluded: chain B residue 502 MET 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: 4.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 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 = 0.3226 r_free = 0.3226 target = 0.119012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.101846 restraints weight = 8655.754| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.84 r_work: 0.2921 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3151 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= 0.225 Angle : 0.512 5.662 10006 Z= 0.268 Chirality : 0.041 0.141 1170 Planarity : 0.006 0.059 1224 Dihedral : 3.629 13.881 978 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.89 % Allowed : 9.58 % 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: 2.84 (0.28), residues: 922 helix: 2.79 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.67 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 B 137 ARG 0.002 0.000 ARG A 304 *********************** 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 136 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8654 (t0) cc_final: 0.8210 (t0) REVERT: A 346 LYS cc_start: 0.8084 (mttt) cc_final: 0.7640 (mptt) REVERT: A 410 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7555 (ttt) REVERT: A 583 GLN cc_start: 0.7326 (mt0) cc_final: 0.6958 (tt0) REVERT: B 325 ASP cc_start: 0.8651 (t0) cc_final: 0.8210 (t0) REVERT: B 346 LYS cc_start: 0.8083 (mttt) cc_final: 0.7641 (mptt) REVERT: B 410 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7560 (ttt) REVERT: B 583 GLN cc_start: 0.7296 (mt0) cc_final: 0.6926 (tt0) outliers start: 22 outliers final: 20 residues processed: 124 average time/residue: 0.1385 time to fit residues: 25.4661 Evaluate side-chains 133 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 339 MET Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 501 ILE 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 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 501 ILE 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: 0.9980 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.117006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099778 restraints weight = 8698.773| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.84 r_work: 0.2892 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7352 Z= 0.265 Angle : 0.540 5.792 10006 Z= 0.281 Chirality : 0.042 0.141 1170 Planarity : 0.006 0.057 1224 Dihedral : 3.640 13.410 978 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.81 % Allowed : 8.92 % Favored : 87.27 % 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: 2.72 (0.28), residues: 922 helix: 2.68 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.69 (0.40), 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 B 547 TYR 0.008 0.001 TYR B 137 ARG 0.002 0.000 ARG B 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 140 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7696 (t80) REVERT: A 295 THR cc_start: 0.8981 (m) cc_final: 0.8605 (t) REVERT: A 325 ASP cc_start: 0.8641 (t0) cc_final: 0.8166 (t0) REVERT: A 410 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7498 (ttt) REVERT: A 583 GLN cc_start: 0.7288 (mt0) cc_final: 0.6897 (tt0) REVERT: B 235 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7695 (t80) REVERT: B 295 THR cc_start: 0.8978 (m) cc_final: 0.8599 (t) REVERT: B 325 ASP cc_start: 0.8642 (t0) cc_final: 0.8111 (t0) REVERT: B 410 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7509 (ttt) REVERT: B 583 GLN cc_start: 0.7284 (mt0) cc_final: 0.6885 (tt0) outliers start: 29 outliers final: 23 residues processed: 128 average time/residue: 0.1313 time to fit residues: 25.4096 Evaluate side-chains 135 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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 A residue 556 ILE 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 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 536 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 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 = 0.3213 r_free = 0.3213 target = 0.117910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100689 restraints weight = 8678.032| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.87 r_work: 0.2905 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3282 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= 0.238 Angle : 0.521 6.442 10006 Z= 0.272 Chirality : 0.041 0.140 1170 Planarity : 0.006 0.058 1224 Dihedral : 3.626 13.674 978 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.81 % Allowed : 9.32 % Favored : 86.88 % 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: 2.75 (0.28), residues: 922 helix: 2.71 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.002 0.001 HIS A 451 PHE 0.028 0.002 PHE B 547 TYR 0.008 0.001 TYR A 137 ARG 0.001 0.000 ARG A 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 : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7751 (t80) REVERT: A 325 ASP cc_start: 0.8694 (t0) cc_final: 0.8219 (t0) REVERT: A 410 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7609 (ttt) REVERT: A 583 GLN cc_start: 0.7379 (mt0) cc_final: 0.6974 (tt0) REVERT: B 235 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7755 (t80) REVERT: B 325 ASP cc_start: 0.8693 (t0) cc_final: 0.8160 (t0) REVERT: B 410 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7613 (ttt) REVERT: B 583 GLN cc_start: 0.7380 (mt0) cc_final: 0.6968 (tt0) outliers start: 29 outliers final: 25 residues processed: 125 average time/residue: 0.1598 time to fit residues: 29.8406 Evaluate side-chains 132 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 A residue 556 ILE 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 536 VAL 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: 2.9990 chunk 30 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 17 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 = 0.3214 r_free = 0.3214 target = 0.117979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.100855 restraints weight = 8704.461| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.84 r_work: 0.2906 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7352 Z= 0.238 Angle : 0.530 7.113 10006 Z= 0.276 Chirality : 0.041 0.141 1170 Planarity : 0.006 0.057 1224 Dihedral : 3.620 13.555 978 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.94 % Allowed : 9.06 % Favored : 87.01 % 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: 2.74 (0.28), residues: 922 helix: 2.70 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.67 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.002 0.001 HIS A 451 PHE 0.028 0.001 PHE A 547 TYR 0.008 0.001 TYR A 137 ARG 0.002 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 137 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8326 (tp40) REVERT: A 235 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7651 (t80) REVERT: A 325 ASP cc_start: 0.8672 (t0) cc_final: 0.8158 (t0) REVERT: A 410 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7476 (ttt) REVERT: B 152 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8325 (tp40) REVERT: B 235 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7660 (t80) REVERT: B 295 THR cc_start: 0.8992 (m) cc_final: 0.8660 (t) REVERT: B 325 ASP cc_start: 0.8679 (t0) cc_final: 0.8171 (t0) REVERT: B 410 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7473 (ttt) outliers start: 30 outliers final: 24 residues processed: 124 average time/residue: 0.1298 time to fit residues: 24.4679 Evaluate side-chains 133 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 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 536 VAL 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: 0.5980 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 0.0370 chunk 37 optimal weight: 0.5980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 = 0.121670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.104374 restraints weight = 8686.493| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.85 r_work: 0.2959 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3505 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= 0.172 Angle : 0.503 7.965 10006 Z= 0.260 Chirality : 0.040 0.141 1170 Planarity : 0.005 0.057 1224 Dihedral : 3.542 14.301 978 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.02 % Allowed : 10.63 % 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: 3.03 (0.28), residues: 922 helix: 2.89 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.50 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 469 HIS 0.001 0.001 HIS B 451 PHE 0.027 0.001 PHE B 547 TYR 0.006 0.001 TYR A 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 132 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8311 (tp40) REVERT: A 235 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7658 (t80) REVERT: B 152 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8317 (tp40) REVERT: B 235 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7663 (t80) outliers start: 23 outliers final: 21 residues processed: 122 average time/residue: 0.1295 time to fit residues: 24.0014 Evaluate side-chains 128 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 262 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 339 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 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 235 PHE 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 457 VAL Chi-restraints excluded: chain B residue 477 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 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: 0.7980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.119337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.102021 restraints weight = 8666.201| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.84 r_work: 0.2929 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7352 Z= 0.234 Angle : 0.525 7.834 10006 Z= 0.274 Chirality : 0.042 0.137 1170 Planarity : 0.006 0.056 1224 Dihedral : 3.522 14.207 978 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.28 % Allowed : 10.63 % Favored : 86.09 % 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: 2.84 (0.28), residues: 922 helix: 2.78 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.66 (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 B 547 TYR 0.007 0.001 TYR A 137 ARG 0.001 0.000 ARG B 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3283.78 seconds wall clock time: 59 minutes 10.80 seconds (3550.80 seconds total)