Starting phenix.real_space_refine on Sat Jul 26 07:24:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n59_48918/07_2025/9n59_48918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n59_48918/07_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_48918/07_2025/9n59_48918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n59_48918/07_2025/9n59_48918.map" model { file = "/net/cci-nas-00/data/ceres_data/9n59_48918/07_2025/9n59_48918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n59_48918/07_2025/9n59_48918.cif" } resolution = 2.82 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 24.78, per 1000 atoms: 3.06 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.93 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: 2.65 Time building geometry restraints manager: 2.80 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3042.860 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: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 42.690 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3099.280 ------------------------------------------------------------------------------- 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 : 9.13 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 (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: 1.36 (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 HIS 0.002 0.001 HIS A 388 PHE 0.040 0.002 PHE B 242 TYR 0.016 0.001 TYR B 531 ARG 0.008 0.001 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.12645 ( 517) hydrogen bonds : angle 5.68999 ( 1461) covalent geometry : bond 0.00346 ( 8144) covalent geometry : angle 0.56111 (11102) *********************** 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 : 0.923 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 1.2324 time to fit residues: 83.0836 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 : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 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 99 GLN B 100 ASN ** B 323 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 = 0.4447 r_free = 0.4447 target = 0.157435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106827 restraints weight = 14882.174| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.26 r_work: 0.3390 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8144 Z= 0.109 Angle : 0.459 7.121 11102 Z= 0.250 Chirality : 0.037 0.167 1394 Planarity : 0.003 0.042 1482 Dihedral : 4.006 41.566 1184 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.29 % Allowed : 17.09 % Favored : 80.62 % 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: 1.72 (0.26), residues: 1124 helix: 3.40 (0.23), residues: 490 sheet: -0.47 (0.38), residues: 189 loop : -0.79 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 388 PHE 0.012 0.001 PHE A 330 TYR 0.016 0.001 TYR B 531 ARG 0.002 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 517) hydrogen bonds : angle 4.71081 ( 1461) covalent geometry : bond 0.00202 ( 8144) covalent geometry : angle 0.45877 (11102) *********************** 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 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.907 Fit side-chains REVERT: A 128 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8278 (mm-30) REVERT: B 4 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6224 (mm) outliers start: 20 outliers final: 8 residues processed: 81 average time/residue: 0.9384 time to fit residues: 82.7192 Evaluate side-chains 71 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE 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 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 18 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 161 GLN A 542 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.158093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.107533 restraints weight = 15102.432| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.34 r_work: 0.3435 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8144 Z= 0.096 Angle : 0.434 7.740 11102 Z= 0.234 Chirality : 0.036 0.164 1394 Planarity : 0.003 0.039 1482 Dihedral : 3.802 37.950 1184 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.64 % Allowed : 16.86 % Favored : 80.50 % 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: 1.98 (0.26), residues: 1124 helix: 3.69 (0.22), residues: 484 sheet: -0.35 (0.38), residues: 189 loop : -0.67 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 388 PHE 0.008 0.001 PHE B 330 TYR 0.013 0.001 TYR B 531 ARG 0.003 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 517) hydrogen bonds : angle 4.46579 ( 1461) covalent geometry : bond 0.00176 ( 8144) covalent geometry : angle 0.43399 (11102) *********************** 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 94 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.916 Fit side-chains REVERT: A 128 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8294 (mm-30) REVERT: B 4 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6320 (mm) outliers start: 23 outliers final: 11 residues processed: 89 average time/residue: 0.8620 time to fit residues: 83.8194 Evaluate side-chains 72 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 452 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 440 VAL Chi-restraints excluded: chain B residue 558 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 80 optimal weight: 0.0370 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 30.0000 chunk 47 optimal weight: 0.0970 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** 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 = 0.4467 r_free = 0.4467 target = 0.158386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107888 restraints weight = 15020.059| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.29 r_work: 0.3416 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8144 Z= 0.093 Angle : 0.452 11.536 11102 Z= 0.236 Chirality : 0.036 0.163 1394 Planarity : 0.003 0.038 1482 Dihedral : 3.693 33.975 1184 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.75 % Allowed : 17.43 % Favored : 79.82 % 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: 2.06 (0.26), residues: 1124 helix: 3.75 (0.22), residues: 483 sheet: -0.23 (0.39), residues: 189 loop : -0.66 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 388 PHE 0.014 0.001 PHE A 330 TYR 0.012 0.001 TYR B 531 ARG 0.002 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 517) hydrogen bonds : angle 4.34033 ( 1461) covalent geometry : bond 0.00170 ( 8144) covalent geometry : angle 0.45169 (11102) *********************** 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 93 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.953 Fit side-chains REVERT: A 128 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8281 (mm-30) REVERT: B 21 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8153 (tp-100) outliers start: 24 outliers final: 14 residues processed: 85 average time/residue: 0.8424 time to fit residues: 78.3845 Evaluate side-chains 79 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 B residue 21 GLN 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 531 TYR 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 6 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 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 = 0.4451 r_free = 0.4451 target = 0.157111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.106121 restraints weight = 14729.137| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.27 r_work: 0.3378 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8144 Z= 0.116 Angle : 0.464 9.329 11102 Z= 0.243 Chirality : 0.037 0.165 1394 Planarity : 0.003 0.038 1482 Dihedral : 3.732 31.045 1184 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.75 % Allowed : 17.66 % Favored : 79.59 % 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 (0.26), residues: 1124 helix: 3.57 (0.22), residues: 491 sheet: -0.23 (0.38), residues: 193 loop : -0.71 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 388 PHE 0.008 0.001 PHE A 330 TYR 0.013 0.001 TYR B 531 ARG 0.002 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 517) hydrogen bonds : angle 4.36460 ( 1461) covalent geometry : bond 0.00244 ( 8144) covalent geometry : angle 0.46393 (11102) *********************** 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 93 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8295 (mm-30) REVERT: A 373 ASP cc_start: 0.8825 (m-30) cc_final: 0.8158 (t70) REVERT: B 21 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8226 (tp-100) REVERT: B 218 MET cc_start: 0.8860 (mmm) cc_final: 0.8476 (mmm) outliers start: 24 outliers final: 19 residues processed: 84 average time/residue: 0.8496 time to fit residues: 78.1142 Evaluate side-chains 83 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 21 GLN 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 531 TYR 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 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 47 optimal weight: 0.1980 chunk 18 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 73 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 overall best weight: 0.3944 ------------------------------------------------------------------------------- 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 = 0.4457 r_free = 0.4457 target = 0.157280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104296 restraints weight = 14908.604| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.89 r_work: 0.3482 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8144 Z= 0.093 Angle : 0.456 10.863 11102 Z= 0.239 Chirality : 0.036 0.164 1394 Planarity : 0.002 0.035 1482 Dihedral : 3.608 27.439 1184 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.98 % Allowed : 17.89 % 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 (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: 2.13 (0.26), residues: 1124 helix: 3.76 (0.22), residues: 486 sheet: -0.06 (0.39), residues: 189 loop : -0.65 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 388 PHE 0.014 0.001 PHE A 330 TYR 0.012 0.001 TYR B 531 ARG 0.002 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 517) hydrogen bonds : angle 4.23857 ( 1461) covalent geometry : bond 0.00173 ( 8144) covalent geometry : angle 0.45605 (11102) *********************** 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 95 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8220 (mm-30) REVERT: B 21 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8158 (tp-100) outliers start: 26 outliers final: 20 residues processed: 86 average time/residue: 1.1288 time to fit residues: 105.1859 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 428 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 21 GLN 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 230 VAL 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 388 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 531 TYR 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 39 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 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 = 0.4428 r_free = 0.4428 target = 0.154352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.099184 restraints weight = 14812.460| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.91 r_work: 0.3418 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8144 Z= 0.137 Angle : 0.491 10.599 11102 Z= 0.255 Chirality : 0.038 0.196 1394 Planarity : 0.003 0.036 1482 Dihedral : 3.736 25.859 1184 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.98 % Allowed : 18.69 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.26), residues: 1124 helix: 3.45 (0.22), residues: 491 sheet: -0.14 (0.38), residues: 195 loop : -0.74 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 388 PHE 0.010 0.001 PHE B 330 TYR 0.015 0.001 TYR B 531 ARG 0.002 0.000 ARG B 525 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 517) hydrogen bonds : angle 4.30569 ( 1461) covalent geometry : bond 0.00294 ( 8144) covalent geometry : angle 0.49143 (11102) *********************** 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 92 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8338 (mm-30) REVERT: A 387 MET cc_start: 0.5555 (mmm) cc_final: 0.5253 (tpp) REVERT: B 21 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8250 (tp-100) REVERT: B 393 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.7997 (p) outliers start: 26 outliers final: 22 residues processed: 81 average time/residue: 0.7719 time to fit residues: 68.9462 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 21 GLN 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 230 VAL 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 393 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 111 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 0.0020 overall best weight: 1.7992 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.154232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099751 restraints weight = 14976.186| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.89 r_work: 0.3385 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8144 Z= 0.139 Angle : 0.491 10.891 11102 Z= 0.256 Chirality : 0.038 0.168 1394 Planarity : 0.003 0.035 1482 Dihedral : 3.802 25.436 1184 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.21 % Allowed : 18.35 % Favored : 78.44 % 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: 1.86 (0.26), residues: 1124 helix: 3.42 (0.22), residues: 492 sheet: -0.06 (0.39), residues: 189 loop : -0.77 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.014 0.001 PHE B 330 TYR 0.014 0.001 TYR B 531 ARG 0.002 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 517) hydrogen bonds : angle 4.30735 ( 1461) covalent geometry : bond 0.00300 ( 8144) covalent geometry : angle 0.49107 (11102) *********************** 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 94 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8321 (mm-30) REVERT: B 15 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.5994 (ttmt) REVERT: B 222 MET cc_start: 0.7869 (mmm) cc_final: 0.6748 (mmm) outliers start: 28 outliers final: 21 residues processed: 82 average time/residue: 0.7931 time to fit residues: 71.8713 Evaluate side-chains 84 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 B residue 15 LYS Chi-restraints excluded: chain B residue 53 MET 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 230 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 0.0470 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 388 HIS ** B 323 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 = 0.4440 r_free = 0.4440 target = 0.155810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.101794 restraints weight = 15191.576| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.91 r_work: 0.3410 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2198 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= 0.101 Angle : 0.482 11.110 11102 Z= 0.248 Chirality : 0.037 0.163 1394 Planarity : 0.003 0.035 1482 Dihedral : 3.666 22.283 1184 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.52 % Allowed : 19.15 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.26), residues: 1124 helix: 3.57 (0.23), residues: 492 sheet: -0.02 (0.39), residues: 189 loop : -0.74 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 388 PHE 0.013 0.001 PHE B 330 TYR 0.013 0.001 TYR B 531 ARG 0.003 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 517) hydrogen bonds : angle 4.20024 ( 1461) covalent geometry : bond 0.00195 ( 8144) covalent geometry : angle 0.48165 (11102) *********************** 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 86 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.5675 (mmm) cc_final: 0.5304 (tpp) REVERT: B 15 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6035 (tttt) outliers start: 22 outliers final: 20 residues processed: 79 average time/residue: 0.8485 time to fit residues: 73.4137 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 : 0.840 ------------------------------------------------------------------------------- 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 B residue 15 LYS 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 230 VAL 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 8 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.4417 r_free = 0.4417 target = 0.153991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.102874 restraints weight = 14858.270| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.27 r_work: 0.3334 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8144 Z= 0.159 Angle : 0.516 12.198 11102 Z= 0.266 Chirality : 0.039 0.172 1394 Planarity : 0.003 0.036 1482 Dihedral : 3.873 23.911 1184 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.75 % Allowed : 19.72 % Favored : 77.52 % 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: 1.86 (0.26), residues: 1124 helix: 3.40 (0.22), residues: 492 sheet: -0.13 (0.39), residues: 195 loop : -0.72 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 388 PHE 0.032 0.002 PHE B 242 TYR 0.014 0.001 TYR B 531 ARG 0.004 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 517) hydrogen bonds : angle 4.32762 ( 1461) covalent geometry : bond 0.00350 ( 8144) covalent geometry : angle 0.51612 (11102) ********************** 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 88 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6106 (ttmt) REVERT: B 222 MET cc_start: 0.7834 (mmt) cc_final: 0.6928 (mmm) REVERT: B 347 LEU cc_start: 0.7356 (tm) cc_final: 0.7114 (tt) REVERT: B 393 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8036 (p) outliers start: 24 outliers final: 20 residues processed: 79 average time/residue: 0.8225 time to fit residues: 71.8065 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 : 0.985 ------------------------------------------------------------------------------- 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 B residue 15 LYS 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 230 VAL 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 393 SER 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 11 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 0.1980 chunk 73 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4442 r_free = 0.4442 target = 0.156583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106589 restraints weight = 15205.373| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.25 r_work: 0.3424 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8144 Z= 0.103 Angle : 0.490 11.761 11102 Z= 0.252 Chirality : 0.038 0.163 1394 Planarity : 0.002 0.035 1482 Dihedral : 3.724 21.505 1184 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.41 % Allowed : 20.07 % Favored : 77.52 % 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 (0.26), residues: 1124 helix: 3.59 (0.23), residues: 492 sheet: -0.15 (0.38), residues: 199 loop : -0.81 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 388 PHE 0.011 0.001 PHE B 330 TYR 0.012 0.001 TYR B 531 ARG 0.004 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 517) hydrogen bonds : angle 4.22444 ( 1461) covalent geometry : bond 0.00201 ( 8144) covalent geometry : angle 0.48990 (11102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18213.48 seconds wall clock time: 324 minutes 55.99 seconds (19495.99 seconds total)