Starting phenix.real_space_refine on Wed Sep 17 11:34:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n59_48918/09_2025/9n59_48918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n59_48918/09_2025/9n59_48918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n59_48918/09_2025/9n59_48918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n59_48918/09_2025/9n59_48918.map" model { file = "/net/cci-nas-00/data/ceres_data/9n59_48918/09_2025/9n59_48918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n59_48918/09_2025/9n59_48918.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 4874 2.51 5 N 1380 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8088 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4044 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 559} Chain: "B" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4044 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 559} Time building chain proxies: 1.77, per 1000 atoms: 0.22 Number of scatterers: 8088 At special positions: 0 Unit cell: (91.65, 113.75, 267.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 1820 8.00 N 1380 7.00 C 4874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 421.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 15 sheets defined 44.4% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 7 through 34 Processing helix chain 'A' and resid 43 through 99 Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.659A pdb=" N GLU A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 325 through 336 removed outlier: 4.294A pdb=" N LEU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 479 through 528 Processing helix chain 'A' and resid 530 through 558 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.904A pdb=" N SER A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 34 Processing helix chain 'B' and resid 43 through 99 Processing helix chain 'B' and resid 104 through 129 removed outlier: 3.623A pdb=" N GLU B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.713A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 479 through 528 removed outlier: 3.509A pdb=" N ILE B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 556 Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.546A pdb=" N SER B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 146 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 184 removed outlier: 4.165A pdb=" N SER A 183 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 197 removed outlier: 6.389A pdb=" N THR A 426 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN A 443 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR A 428 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 212 removed outlier: 3.935A pdb=" N ASP A 211 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.706A pdb=" N SER A 346 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR A 353 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR A 366 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR A 252 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU A 239 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 227 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 146 Processing sheet with id=AA8, first strand: chain 'B' and resid 196 through 197 removed outlier: 6.732A pdb=" N THR B 426 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN B 443 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR B 428 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 211 through 212 Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 239 removed outlier: 3.682A pdb=" N VAL B 227 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AB3, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.956A pdb=" N ASN B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 282 " --> pdb=" O ASN B 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AB5, first strand: chain 'B' and resid 306 through 307 Processing sheet with id=AB6, first strand: chain 'B' and resid 459 through 460 517 hydrogen bonds defined for protein. 1461 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: 1.51 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2880 1.34 - 1.46: 1700 1.46 - 1.58: 3536 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 8144 Sorted by residual: bond pdb=" C VAL B 558 " pdb=" N PRO B 559 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.73e+00 bond pdb=" CA VAL A 558 " pdb=" C VAL A 558 " ideal model delta sigma weight residual 1.520 1.532 -0.012 8.80e-03 1.29e+04 1.92e+00 bond pdb=" CA VAL B 558 " pdb=" CB VAL B 558 " ideal model delta sigma weight residual 1.534 1.544 -0.009 6.80e-03 2.16e+04 1.78e+00 bond pdb=" CA VAL A 558 " pdb=" CB VAL A 558 " ideal model delta sigma weight residual 1.534 1.544 -0.009 6.80e-03 2.16e+04 1.75e+00 bond pdb=" CA VAL B 558 " pdb=" C VAL B 558 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.66e+00 ... (remaining 8139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 11035 2.71 - 5.42: 55 5.42 - 8.13: 10 8.13 - 10.84: 1 10.84 - 13.54: 1 Bond angle restraints: 11102 Sorted by residual: angle pdb=" CA LEU B 347 " pdb=" CB LEU B 347 " pdb=" CG LEU B 347 " ideal model delta sigma weight residual 116.30 129.84 -13.54 3.50e+00 8.16e-02 1.50e+01 angle pdb=" C VAL A 558 " pdb=" CA VAL A 558 " pdb=" CB VAL A 558 " ideal model delta sigma weight residual 114.35 110.30 4.05 1.06e+00 8.90e-01 1.46e+01 angle pdb=" CB MET A 387 " pdb=" CG MET A 387 " pdb=" SD MET A 387 " ideal model delta sigma weight residual 112.70 123.21 -10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N ALA B 379 " pdb=" CA ALA B 379 " pdb=" C ALA B 379 " ideal model delta sigma weight residual 114.04 110.05 3.99 1.24e+00 6.50e-01 1.03e+01 angle pdb=" CB LYS A 297 " pdb=" CG LYS A 297 " pdb=" CD LYS A 297 " ideal model delta sigma weight residual 111.30 105.19 6.11 2.30e+00 1.89e-01 7.05e+00 ... (remaining 11097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4311 17.35 - 34.70: 424 34.70 - 52.05: 98 52.05 - 69.40: 29 69.40 - 86.75: 8 Dihedral angle restraints: 4870 sinusoidal: 1670 harmonic: 3200 Sorted by residual: dihedral pdb=" CA ASN B 182 " pdb=" C ASN B 182 " pdb=" N SER B 183 " pdb=" CA SER B 183 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ALA B 344 " pdb=" C ALA B 344 " pdb=" N ARG B 345 " pdb=" CA ARG B 345 " ideal model delta harmonic sigma weight residual -180.00 -161.71 -18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ILE A 526 " pdb=" C ILE A 526 " pdb=" N GLU A 527 " pdb=" CA GLU A 527 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 4867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 861 0.028 - 0.055: 358 0.055 - 0.083: 111 0.083 - 0.110: 47 0.110 - 0.138: 17 Chirality restraints: 1394 Sorted by residual: chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE A 157 " pdb=" N ILE A 157 " pdb=" C ILE A 157 " pdb=" CB ILE A 157 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ASN B 182 " pdb=" N ASN B 182 " pdb=" C ASN B 182 " pdb=" CB ASN B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1391 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 242 " -0.016 2.00e-02 2.50e+03 1.72e-02 5.21e+00 pdb=" CG PHE B 242 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 242 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 242 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 242 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 242 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 180 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C THR A 180 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 180 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN A 181 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 558 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO B 559 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 559 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 559 " -0.027 5.00e-02 4.00e+02 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1458 2.76 - 3.30: 8464 3.30 - 3.83: 13671 3.83 - 4.37: 15472 4.37 - 4.90: 26938 Nonbonded interactions: 66003 Sorted by model distance: nonbonded pdb=" O LEU A 565 " pdb=" OH TYR B 531 " model vdw 2.226 3.040 nonbonded pdb=" O LEU B 17 " pdb=" OG SER B 20 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASN B 243 " pdb=" OG SER B 246 " model vdw 2.237 3.040 nonbonded pdb=" OE1 GLU B 130 " pdb=" NZ LYS B 135 " model vdw 2.307 3.120 nonbonded pdb=" O LEU A 31 " pdb=" OH TYR A 531 " model vdw 2.315 3.040 ... (remaining 65998 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: 0.02 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: 90.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.000 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: 0.010 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8144 Z= 0.167 Angle : 0.561 13.544 11102 Z= 0.306 Chirality : 0.037 0.138 1394 Planarity : 0.003 0.046 1482 Dihedral : 15.460 86.752 2822 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 17.78 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.26), residues: 1124 helix: 3.00 (0.23), residues: 485 sheet: -0.82 (0.37), residues: 196 loop : -0.68 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 65 TYR 0.016 0.001 TYR B 531 PHE 0.040 0.002 PHE B 242 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8144) covalent geometry : angle 0.56111 (11102) hydrogen bonds : bond 0.12645 ( 517) hydrogen bonds : angle 5.68999 ( 1461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.290 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.5622 time to fit residues: 37.6957 Evaluate side-chains 55 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 100 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.149939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094650 restraints weight = 14390.376| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.19 r_work: 0.3383 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8144 Z= 0.142 Angle : 0.481 7.483 11102 Z= 0.261 Chirality : 0.038 0.168 1394 Planarity : 0.003 0.044 1482 Dihedral : 4.120 43.072 1184 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.41 % Allowed : 17.43 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.26), residues: 1124 helix: 3.28 (0.23), residues: 490 sheet: -0.54 (0.38), residues: 189 loop : -0.83 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.018 0.001 TYR B 531 PHE 0.012 0.001 PHE A 330 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8144) covalent geometry : angle 0.48109 (11102) hydrogen bonds : bond 0.04966 ( 517) hydrogen bonds : angle 4.83722 ( 1461) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.319 Fit side-chains REVERT: A 128 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8356 (mm-30) REVERT: B 4 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6199 (mm) outliers start: 21 outliers final: 10 residues processed: 76 average time/residue: 0.4475 time to fit residues: 36.7763 Evaluate side-chains 67 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN B 161 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.157382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.107213 restraints weight = 14855.186| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.29 r_work: 0.3392 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8144 Z= 0.099 Angle : 0.436 8.612 11102 Z= 0.236 Chirality : 0.037 0.163 1394 Planarity : 0.003 0.041 1482 Dihedral : 3.908 39.118 1184 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.10 % Allowed : 16.51 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.26), residues: 1124 helix: 3.52 (0.23), residues: 490 sheet: -0.38 (0.38), residues: 189 loop : -0.75 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 465 TYR 0.014 0.001 TYR B 531 PHE 0.007 0.001 PHE A 330 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 8144) covalent geometry : angle 0.43646 (11102) hydrogen bonds : bond 0.04276 ( 517) hydrogen bonds : angle 4.53273 ( 1461) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.304 Fit side-chains REVERT: A 128 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8292 (mm-30) REVERT: B 4 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6297 (mm) outliers start: 27 outliers final: 16 residues processed: 89 average time/residue: 0.4299 time to fit residues: 41.3346 Evaluate side-chains 80 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 531 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 99 GLN B 127 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.153311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093280 restraints weight = 15221.914| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.00 r_work: 0.3370 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8144 Z= 0.176 Angle : 0.505 11.767 11102 Z= 0.263 Chirality : 0.038 0.175 1394 Planarity : 0.003 0.043 1482 Dihedral : 4.045 37.499 1184 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.21 % Allowed : 17.66 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.26), residues: 1124 helix: 3.33 (0.22), residues: 486 sheet: -0.36 (0.38), residues: 191 loop : -0.80 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.017 0.001 TYR B 531 PHE 0.014 0.001 PHE A 330 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8144) covalent geometry : angle 0.50531 (11102) hydrogen bonds : bond 0.04829 ( 517) hydrogen bonds : angle 4.60350 ( 1461) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.313 Fit side-chains REVERT: A 128 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8393 (mm-30) REVERT: A 373 ASP cc_start: 0.8881 (m-30) cc_final: 0.8178 (t0) REVERT: A 557 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8298 (tp40) REVERT: B 4 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6219 (mm) REVERT: B 21 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: B 212 GLU cc_start: 0.9009 (pm20) cc_final: 0.8651 (pp20) outliers start: 28 outliers final: 20 residues processed: 87 average time/residue: 0.4594 time to fit residues: 43.0095 Evaluate side-chains 85 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 558 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.0020 chunk 78 optimal weight: 20.0000 overall best weight: 2.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.153496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.099829 restraints weight = 14929.400| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.86 r_work: 0.3340 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8144 Z= 0.203 Angle : 0.522 8.678 11102 Z= 0.274 Chirality : 0.040 0.192 1394 Planarity : 0.003 0.041 1482 Dihedral : 4.168 36.419 1184 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.67 % Allowed : 18.23 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.26), residues: 1124 helix: 3.14 (0.22), residues: 486 sheet: -0.39 (0.38), residues: 191 loop : -0.84 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.019 0.002 TYR B 531 PHE 0.009 0.001 PHE B 330 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8144) covalent geometry : angle 0.52174 (11102) hydrogen bonds : bond 0.04975 ( 517) hydrogen bonds : angle 4.69901 ( 1461) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8469 (mm-30) REVERT: B 4 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6172 (mm) REVERT: B 21 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: B 212 GLU cc_start: 0.8908 (pm20) cc_final: 0.8655 (pp20) outliers start: 32 outliers final: 23 residues processed: 95 average time/residue: 0.4366 time to fit residues: 45.0155 Evaluate side-chains 91 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 558 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.148063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091186 restraints weight = 14355.469| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.86 r_work: 0.3356 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8144 Z= 0.141 Angle : 0.485 8.655 11102 Z= 0.257 Chirality : 0.038 0.166 1394 Planarity : 0.003 0.038 1482 Dihedral : 4.034 33.967 1184 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.33 % Allowed : 18.58 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.26), residues: 1124 helix: 3.25 (0.23), residues: 490 sheet: -0.37 (0.39), residues: 189 loop : -0.79 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 465 TYR 0.017 0.001 TYR B 531 PHE 0.016 0.001 PHE A 330 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8144) covalent geometry : angle 0.48514 (11102) hydrogen bonds : bond 0.04592 ( 517) hydrogen bonds : angle 4.56309 ( 1461) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8443 (mm-30) REVERT: B 4 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6139 (mm) REVERT: B 21 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7860 (tm-30) outliers start: 29 outliers final: 24 residues processed: 87 average time/residue: 0.4715 time to fit residues: 44.2295 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 558 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.155576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104109 restraints weight = 15147.707| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.81 r_work: 0.3405 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8144 Z= 0.108 Angle : 0.467 10.228 11102 Z= 0.244 Chirality : 0.037 0.176 1394 Planarity : 0.003 0.036 1482 Dihedral : 3.867 30.050 1184 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.78 % Allowed : 18.81 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.26), residues: 1124 helix: 3.45 (0.23), residues: 490 sheet: -0.30 (0.39), residues: 189 loop : -0.75 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.015 0.001 TYR B 531 PHE 0.011 0.001 PHE A 330 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8144) covalent geometry : angle 0.46662 (11102) hydrogen bonds : bond 0.04210 ( 517) hydrogen bonds : angle 4.42139 ( 1461) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8333 (mm-30) REVERT: B 4 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6225 (mm) REVERT: B 21 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: B 218 MET cc_start: 0.8698 (mmm) cc_final: 0.8468 (mpm) REVERT: B 442 ASP cc_start: 0.8010 (t70) cc_final: 0.7808 (t0) REVERT: B 473 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7850 (mmmm) outliers start: 33 outliers final: 22 residues processed: 89 average time/residue: 0.4183 time to fit residues: 40.5311 Evaluate side-chains 86 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 558 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 45 optimal weight: 0.0010 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 99 optimal weight: 0.0370 overall best weight: 0.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.157045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.105926 restraints weight = 14995.483| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.80 r_work: 0.3428 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8144 Z= 0.097 Angle : 0.454 9.063 11102 Z= 0.242 Chirality : 0.037 0.161 1394 Planarity : 0.003 0.036 1482 Dihedral : 3.788 26.709 1184 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.10 % Allowed : 19.95 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.26), residues: 1124 helix: 3.63 (0.22), residues: 484 sheet: -0.23 (0.39), residues: 189 loop : -0.67 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 345 TYR 0.014 0.001 TYR B 531 PHE 0.017 0.001 PHE A 330 HIS 0.005 0.002 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 8144) covalent geometry : angle 0.45390 (11102) hydrogen bonds : bond 0.04000 ( 517) hydrogen bonds : angle 4.35601 ( 1461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8256 (mm-30) REVERT: B 218 MET cc_start: 0.8796 (mmm) cc_final: 0.8419 (mpm) outliers start: 27 outliers final: 22 residues processed: 87 average time/residue: 0.4184 time to fit residues: 39.6863 Evaluate side-chains 83 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 558 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 0.0020 chunk 13 optimal weight: 0.0050 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.157104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.106294 restraints weight = 15093.334| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.81 r_work: 0.3479 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8144 Z= 0.096 Angle : 0.471 11.739 11102 Z= 0.245 Chirality : 0.037 0.226 1394 Planarity : 0.003 0.036 1482 Dihedral : 3.677 23.082 1184 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.52 % Allowed : 20.99 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.26), residues: 1124 helix: 3.79 (0.22), residues: 479 sheet: -0.19 (0.39), residues: 189 loop : -0.63 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.013 0.001 TYR B 531 PHE 0.037 0.001 PHE B 242 HIS 0.003 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 8144) covalent geometry : angle 0.47070 (11102) hydrogen bonds : bond 0.03879 ( 517) hydrogen bonds : angle 4.28001 ( 1461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8247 (mm-30) REVERT: B 222 MET cc_start: 0.7714 (mmt) cc_final: 0.6852 (mmm) outliers start: 22 outliers final: 19 residues processed: 80 average time/residue: 0.4397 time to fit residues: 38.0627 Evaluate side-chains 80 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.151575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097025 restraints weight = 14894.323| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.87 r_work: 0.3334 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8144 Z= 0.208 Angle : 0.559 11.655 11102 Z= 0.288 Chirality : 0.040 0.175 1394 Planarity : 0.003 0.038 1482 Dihedral : 4.067 27.811 1184 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.64 % Allowed : 20.87 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.26), residues: 1124 helix: 3.24 (0.22), residues: 487 sheet: -0.26 (0.39), residues: 193 loop : -0.81 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 118 TYR 0.017 0.001 TYR B 531 PHE 0.017 0.002 PHE B 330 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8144) covalent geometry : angle 0.55891 (11102) hydrogen bonds : bond 0.04952 ( 517) hydrogen bonds : angle 4.56679 ( 1461) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.285 Fit side-chains REVERT: A 128 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8469 (mm-30) REVERT: B 78 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8761 (tt0) REVERT: B 222 MET cc_start: 0.7864 (mmt) cc_final: 0.6917 (mmm) outliers start: 23 outliers final: 20 residues processed: 85 average time/residue: 0.4161 time to fit residues: 38.4489 Evaluate side-chains 83 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 89 optimal weight: 0.0170 chunk 71 optimal weight: 0.0170 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.149136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093627 restraints weight = 14505.938| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.85 r_work: 0.3408 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8144 Z= 0.123 Angle : 0.517 11.501 11102 Z= 0.266 Chirality : 0.038 0.163 1394 Planarity : 0.003 0.035 1482 Dihedral : 3.976 26.397 1184 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.75 % Allowed : 21.33 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.26), residues: 1124 helix: 3.40 (0.23), residues: 490 sheet: -0.21 (0.39), residues: 189 loop : -0.79 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 465 TYR 0.015 0.001 TYR B 531 PHE 0.038 0.002 PHE B 242 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8144) covalent geometry : angle 0.51687 (11102) hydrogen bonds : bond 0.04404 ( 517) hydrogen bonds : angle 4.44953 ( 1461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6162.76 seconds wall clock time: 105 minutes 55.75 seconds (6355.75 seconds total)