Starting phenix.real_space_refine on Tue Feb 3 15:23:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nbl_49231/02_2026/9nbl_49231_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nbl_49231/02_2026/9nbl_49231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nbl_49231/02_2026/9nbl_49231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nbl_49231/02_2026/9nbl_49231.map" model { file = "/net/cci-nas-00/data/ceres_data/9nbl_49231/02_2026/9nbl_49231_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nbl_49231/02_2026/9nbl_49231_neut.cif" } resolution = 3.4 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= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 12 5.16 5 C 2671 2.51 5 N 756 2.21 5 O 817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4262 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4206 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 32, 'TRANS': 525} Chain breaks: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.17, per 1000 atoms: 0.27 Number of scatterers: 4262 At special positions: 0 Unit cell: (56.55, 81.25, 85.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 P 4 15.00 Mg 2 11.99 O 817 8.00 N 756 7.00 C 2671 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: 0.41 Conformation dependent library (CDL) restraints added in 285.2 milliseconds 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 4 sheets defined 56.3% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 112 through 130 removed outlier: 3.544A pdb=" N ASN A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.523A pdb=" N LEU A 177 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.591A pdb=" N TYR A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 247 through 263 Processing helix chain 'A' and resid 264 through 269 removed outlier: 5.728A pdb=" N THR A 267 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 314 through 325 removed outlier: 4.137A pdb=" N LEU A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 Processing helix chain 'A' and resid 386 through 402 Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 420 through 439 removed outlier: 3.506A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.684A pdb=" N LEU A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.680A pdb=" N SER A 535 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 558 Processing helix chain 'A' and resid 575 through 584 removed outlier: 4.749A pdb=" N ALA A 581 " --> pdb=" O GLU A 577 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 582 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.856A pdb=" N THR A 15 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 202 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL A 234 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU A 204 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A 236 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA A 206 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 238 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 445 removed outlier: 6.679A pdb=" N LEU A 329 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 495 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET A 331 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL A 497 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET A 333 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 526 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 496 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A 528 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR A 498 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 530 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 529 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 362 217 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.50 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: 1444 1.34 - 1.46: 452 1.46 - 1.57: 2413 1.57 - 1.69: 6 1.69 - 1.81: 20 Bond restraints: 4335 Sorted by residual: bond pdb=" N LEU A 406 " pdb=" CA LEU A 406 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.01e+00 bond pdb=" N ASP A 407 " pdb=" CA ASP A 407 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.37e-02 5.33e+03 6.12e+00 bond pdb=" N GLU A 243 " pdb=" CA GLU A 243 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 4.98e+00 bond pdb=" N ALA A 244 " pdb=" CA ALA A 244 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.32e-02 5.74e+03 4.31e+00 bond pdb=" N ASN A 246 " pdb=" CA ASN A 246 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.50e-02 4.44e+03 3.72e+00 ... (remaining 4330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 5677 1.17 - 2.34: 148 2.34 - 3.51: 48 3.51 - 4.68: 31 4.68 - 5.85: 11 Bond angle restraints: 5915 Sorted by residual: angle pdb=" CA ASP A 407 " pdb=" C ASP A 407 " pdb=" O ASP A 407 " ideal model delta sigma weight residual 121.99 116.82 5.17 1.14e+00 7.69e-01 2.06e+01 angle pdb=" CA ASN A 246 " pdb=" C ASN A 246 " pdb=" O ASN A 246 " ideal model delta sigma weight residual 121.78 117.53 4.25 1.12e+00 7.97e-01 1.44e+01 angle pdb=" CA ALA A 408 " pdb=" C ALA A 408 " pdb=" O ALA A 408 " ideal model delta sigma weight residual 120.92 116.81 4.11 1.12e+00 7.97e-01 1.35e+01 angle pdb=" CA ALA A 245 " pdb=" C ALA A 245 " pdb=" O ALA A 245 " ideal model delta sigma weight residual 120.82 117.14 3.68 1.05e+00 9.07e-01 1.23e+01 angle pdb=" CA LEU A 406 " pdb=" C LEU A 406 " pdb=" O LEU A 406 " ideal model delta sigma weight residual 121.56 117.83 3.73 1.09e+00 8.42e-01 1.17e+01 ... (remaining 5910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 2408 17.57 - 35.14: 167 35.14 - 52.71: 38 52.71 - 70.27: 12 70.27 - 87.84: 6 Dihedral angle restraints: 2631 sinusoidal: 1032 harmonic: 1599 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 27.84 -87.84 1 2.00e+01 2.50e-03 2.31e+01 dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 19.19 -79.19 1 2.00e+01 2.50e-03 1.95e+01 dihedral pdb=" CA ASP A 561 " pdb=" CB ASP A 561 " pdb=" CG ASP A 561 " pdb=" OD1 ASP A 561 " ideal model delta sinusoidal sigma weight residual -30.00 -88.04 58.04 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 2628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 601 0.048 - 0.097: 80 0.097 - 0.145: 29 0.145 - 0.194: 2 0.194 - 0.242: 2 Chirality restraints: 714 Sorted by residual: chirality pdb=" CA PHE A 4 " pdb=" N PHE A 4 " pdb=" C PHE A 4 " pdb=" CB PHE A 4 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA HIS A 327 " pdb=" N HIS A 327 " pdb=" C HIS A 327 " pdb=" CB HIS A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA GLU A 243 " pdb=" N GLU A 243 " pdb=" C GLU A 243 " pdb=" CB GLU A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 711 not shown) Planarity restraints: 762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 538 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 539 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 539 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 539 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 92 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 93 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 503 " -0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 504 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " -0.016 5.00e-02 4.00e+02 ... (remaining 759 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 6 2.51 - 3.11: 3288 3.11 - 3.70: 6546 3.70 - 4.30: 8968 4.30 - 4.90: 15388 Nonbonded interactions: 34196 Sorted by model distance: nonbonded pdb=" O2B ADP A 601 " pdb="MG MG A 603 " model vdw 1.911 2.170 nonbonded pdb=" O2B ADP A 602 " pdb="MG MG A 604 " model vdw 2.146 2.170 nonbonded pdb=" OG1 THR A 23 " pdb="MG MG A 604 " model vdw 2.183 2.170 nonbonded pdb=" OG1 THR A 341 " pdb="MG MG A 603 " model vdw 2.235 2.170 nonbonded pdb=" O GLN A 396 " pdb=" OE1 GLU A 400 " model vdw 2.430 3.040 ... (remaining 34191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.010 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 0.036 4335 Z= 0.156 Angle : 0.616 5.849 5915 Z= 0.317 Chirality : 0.042 0.242 714 Planarity : 0.004 0.045 762 Dihedral : 14.012 87.842 1591 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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 are not related in a simple way. whole: 0.98 (0.38), residues: 550 helix: 2.16 (0.32), residues: 274 sheet: -3.64 (0.53), residues: 72 loop : 0.36 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.007 0.001 TYR A 86 PHE 0.008 0.001 PHE A 163 TRP 0.005 0.001 TRP A 525 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4335) covalent geometry : angle 0.61627 ( 5915) hydrogen bonds : bond 0.15087 ( 217) hydrogen bonds : angle 5.82124 ( 615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8343 (t0) cc_final: 0.8133 (t0) REVERT: A 111 SER cc_start: 0.8395 (m) cc_final: 0.8163 (m) REVERT: A 143 ASP cc_start: 0.8968 (t0) cc_final: 0.8567 (t0) REVERT: A 415 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8036 (tt0) REVERT: A 424 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7390 (tt0) REVERT: A 572 GLU cc_start: 0.7751 (tt0) cc_final: 0.7314 (mt-10) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1009 time to fit residues: 11.6827 Evaluate side-chains 59 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 HIS ** 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 = 0.3698 r_free = 0.3698 target = 0.153794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125026 restraints weight = 4977.594| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.47 r_work: 0.3191 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4335 Z= 0.139 Angle : 0.635 6.047 5915 Z= 0.292 Chirality : 0.043 0.150 714 Planarity : 0.004 0.045 762 Dihedral : 6.580 86.099 612 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.13 % Allowed : 10.61 % Favored : 88.26 % 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 are not related in a simple way. whole: 0.83 (0.38), residues: 550 helix: 1.84 (0.31), residues: 289 sheet: -3.37 (0.54), residues: 72 loop : 0.34 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 290 TYR 0.008 0.001 TYR A 86 PHE 0.011 0.001 PHE A 4 TRP 0.011 0.002 TRP A 160 HIS 0.008 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4335) covalent geometry : angle 0.63454 ( 5915) hydrogen bonds : bond 0.03585 ( 217) hydrogen bonds : angle 4.37546 ( 615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8356 (t0) cc_final: 0.8111 (t0) REVERT: A 100 ASP cc_start: 0.8201 (t70) cc_final: 0.7702 (m-30) REVERT: A 111 SER cc_start: 0.8489 (m) cc_final: 0.8275 (m) REVERT: A 143 ASP cc_start: 0.8902 (t0) cc_final: 0.8509 (t0) REVERT: A 154 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8527 (mm) REVERT: A 257 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 392 GLU cc_start: 0.8252 (tp30) cc_final: 0.7778 (mt-10) REVERT: A 415 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7949 (tt0) REVERT: A 424 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7182 (tt0) REVERT: A 572 GLU cc_start: 0.7662 (tt0) cc_final: 0.7229 (mt-10) outliers start: 5 outliers final: 2 residues processed: 69 average time/residue: 0.0774 time to fit residues: 6.7612 Evaluate side-chains 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 HIS ** 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 = 0.3686 r_free = 0.3686 target = 0.152765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124588 restraints weight = 4919.259| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.43 r_work: 0.3185 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4335 Z= 0.130 Angle : 0.597 5.850 5915 Z= 0.271 Chirality : 0.042 0.163 714 Planarity : 0.004 0.048 762 Dihedral : 6.440 82.027 612 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.90 % Allowed : 10.61 % Favored : 88.49 % 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 are not related in a simple way. whole: 0.79 (0.37), residues: 550 helix: 1.78 (0.30), residues: 290 sheet: -3.19 (0.55), residues: 72 loop : 0.28 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.007 0.001 TYR A 86 PHE 0.011 0.001 PHE A 432 TRP 0.010 0.001 TRP A 160 HIS 0.004 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4335) covalent geometry : angle 0.59715 ( 5915) hydrogen bonds : bond 0.03218 ( 217) hydrogen bonds : angle 3.88571 ( 615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8356 (t0) cc_final: 0.8086 (t0) REVERT: A 111 SER cc_start: 0.8461 (m) cc_final: 0.8246 (m) REVERT: A 143 ASP cc_start: 0.8903 (t0) cc_final: 0.8458 (t0) REVERT: A 154 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8561 (mm) REVERT: A 257 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 392 GLU cc_start: 0.8330 (tp30) cc_final: 0.7768 (tt0) REVERT: A 415 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7977 (tt0) REVERT: A 424 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7203 (tt0) REVERT: A 483 MET cc_start: 0.7762 (tpp) cc_final: 0.7542 (mmm) REVERT: A 572 GLU cc_start: 0.7632 (tt0) cc_final: 0.7199 (mt-10) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.0374 time to fit residues: 3.2826 Evaluate side-chains 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 570 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 HIS ** 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 = 0.3644 r_free = 0.3644 target = 0.148093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120594 restraints weight = 4954.338| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.35 r_work: 0.3146 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4335 Z= 0.203 Angle : 0.638 6.120 5915 Z= 0.294 Chirality : 0.044 0.184 714 Planarity : 0.004 0.050 762 Dihedral : 6.658 84.372 612 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.48 % Allowed : 10.84 % Favored : 86.68 % 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 are not related in a simple way. whole: 0.48 (0.37), residues: 550 helix: 1.53 (0.30), residues: 296 sheet: -3.33 (0.53), residues: 72 loop : 0.08 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.007 0.001 TYR A 86 PHE 0.017 0.001 PHE A 432 TRP 0.009 0.001 TRP A 160 HIS 0.006 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 4335) covalent geometry : angle 0.63832 ( 5915) hydrogen bonds : bond 0.03584 ( 217) hydrogen bonds : angle 3.86777 ( 615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8362 (t0) cc_final: 0.8142 (t0) REVERT: A 100 ASP cc_start: 0.8111 (t70) cc_final: 0.7809 (m-30) REVERT: A 143 ASP cc_start: 0.8991 (t0) cc_final: 0.8484 (t0) REVERT: A 154 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8564 (mm) REVERT: A 361 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8574 (p) REVERT: A 392 GLU cc_start: 0.8413 (tp30) cc_final: 0.7766 (mt-10) REVERT: A 415 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7986 (tt0) REVERT: A 424 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7294 (tt0) REVERT: A 572 GLU cc_start: 0.7709 (tt0) cc_final: 0.7241 (mt-10) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.0596 time to fit residues: 5.0319 Evaluate side-chains 60 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 570 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122665 restraints weight = 4942.703| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.44 r_work: 0.3180 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4335 Z= 0.122 Angle : 0.585 5.965 5915 Z= 0.265 Chirality : 0.041 0.193 714 Planarity : 0.004 0.048 762 Dihedral : 6.520 81.750 612 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.48 % Allowed : 10.84 % Favored : 86.68 % 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 are not related in a simple way. whole: 0.60 (0.36), residues: 550 helix: 1.64 (0.30), residues: 296 sheet: -3.19 (0.53), residues: 72 loop : 0.07 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR A 86 PHE 0.013 0.001 PHE A 432 TRP 0.012 0.001 TRP A 160 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4335) covalent geometry : angle 0.58492 ( 5915) hydrogen bonds : bond 0.03024 ( 217) hydrogen bonds : angle 3.69435 ( 615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8374 (t0) cc_final: 0.8122 (t0) REVERT: A 143 ASP cc_start: 0.8953 (t0) cc_final: 0.8442 (t0) REVERT: A 154 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 369 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7576 (pp) REVERT: A 392 GLU cc_start: 0.8373 (tp30) cc_final: 0.7878 (tt0) REVERT: A 415 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7960 (tt0) REVERT: A 424 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7221 (tt0) REVERT: A 483 MET cc_start: 0.7839 (tpp) cc_final: 0.7415 (mmm) REVERT: A 572 GLU cc_start: 0.7654 (tt0) cc_final: 0.7193 (mt-10) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.0379 time to fit residues: 3.3176 Evaluate side-chains 57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 570 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123045 restraints weight = 5023.000| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.40 r_work: 0.3164 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4335 Z= 0.138 Angle : 0.584 5.933 5915 Z= 0.265 Chirality : 0.041 0.204 714 Planarity : 0.004 0.049 762 Dihedral : 6.475 81.015 612 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.16 % Allowed : 12.19 % Favored : 84.65 % 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 are not related in a simple way. whole: 0.66 (0.36), residues: 550 helix: 1.68 (0.30), residues: 296 sheet: -3.06 (0.54), residues: 72 loop : 0.07 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.005 0.001 TYR A 86 PHE 0.014 0.001 PHE A 432 TRP 0.010 0.001 TRP A 160 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4335) covalent geometry : angle 0.58432 ( 5915) hydrogen bonds : bond 0.03057 ( 217) hydrogen bonds : angle 3.65525 ( 615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8373 (t0) cc_final: 0.8129 (t0) REVERT: A 143 ASP cc_start: 0.8943 (t0) cc_final: 0.8410 (t0) REVERT: A 154 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8527 (mm) REVERT: A 361 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 373 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.5957 (mm) REVERT: A 392 GLU cc_start: 0.8406 (tp30) cc_final: 0.7883 (tt0) REVERT: A 415 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7960 (tt0) REVERT: A 424 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7275 (tt0) REVERT: A 483 MET cc_start: 0.7922 (tpp) cc_final: 0.7537 (mmm) REVERT: A 572 GLU cc_start: 0.7647 (tt0) cc_final: 0.7185 (mt-10) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.0413 time to fit residues: 3.5410 Evaluate side-chains 56 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 448 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.150238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122345 restraints weight = 5010.455| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.46 r_work: 0.3148 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4335 Z= 0.131 Angle : 0.578 5.918 5915 Z= 0.262 Chirality : 0.042 0.217 714 Planarity : 0.004 0.048 762 Dihedral : 6.431 79.820 612 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.93 % Allowed : 13.09 % Favored : 83.97 % 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 are not related in a simple way. whole: 0.74 (0.36), residues: 550 helix: 1.73 (0.30), residues: 296 sheet: -3.03 (0.54), residues: 72 loop : 0.10 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR A 86 PHE 0.014 0.001 PHE A 432 TRP 0.009 0.001 TRP A 160 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4335) covalent geometry : angle 0.57753 ( 5915) hydrogen bonds : bond 0.02947 ( 217) hydrogen bonds : angle 3.62214 ( 615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8382 (t0) cc_final: 0.8142 (t0) REVERT: A 143 ASP cc_start: 0.8945 (t0) cc_final: 0.8435 (t0) REVERT: A 154 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8513 (mm) REVERT: A 361 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8623 (p) REVERT: A 369 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7441 (pp) REVERT: A 373 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.5952 (mm) REVERT: A 392 GLU cc_start: 0.8399 (tp30) cc_final: 0.7853 (tt0) REVERT: A 415 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7962 (tt0) REVERT: A 424 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7253 (tt0) REVERT: A 572 GLU cc_start: 0.7646 (tt0) cc_final: 0.7188 (mt-10) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 0.0527 time to fit residues: 4.1794 Evaluate side-chains 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 448 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119056 restraints weight = 4865.398| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.41 r_work: 0.3154 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4335 Z= 0.146 Angle : 0.583 5.943 5915 Z= 0.264 Chirality : 0.042 0.225 714 Planarity : 0.004 0.048 762 Dihedral : 6.453 79.878 612 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.48 % Allowed : 13.54 % Favored : 83.97 % 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 are not related in a simple way. whole: 0.73 (0.36), residues: 550 helix: 1.70 (0.30), residues: 297 sheet: -3.03 (0.54), residues: 72 loop : 0.15 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR A 86 PHE 0.014 0.001 PHE A 432 TRP 0.008 0.001 TRP A 160 HIS 0.004 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4335) covalent geometry : angle 0.58342 ( 5915) hydrogen bonds : bond 0.03015 ( 217) hydrogen bonds : angle 3.62077 ( 615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8383 (t0) cc_final: 0.8148 (t0) REVERT: A 143 ASP cc_start: 0.8955 (t0) cc_final: 0.8413 (t0) REVERT: A 154 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8515 (mm) REVERT: A 361 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8609 (p) REVERT: A 369 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7544 (pp) REVERT: A 373 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.5954 (mm) REVERT: A 392 GLU cc_start: 0.8416 (tp30) cc_final: 0.7864 (tt0) REVERT: A 415 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7968 (tt0) REVERT: A 424 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7280 (tt0) REVERT: A 572 GLU cc_start: 0.7697 (tt0) cc_final: 0.7233 (mt-10) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.0489 time to fit residues: 3.7848 Evaluate side-chains 57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 34 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122121 restraints weight = 5009.007| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.47 r_work: 0.3163 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4335 Z= 0.125 Angle : 0.570 5.915 5915 Z= 0.257 Chirality : 0.041 0.232 714 Planarity : 0.004 0.048 762 Dihedral : 6.409 78.803 612 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.48 % Allowed : 13.32 % Favored : 84.20 % 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 are not related in a simple way. whole: 0.80 (0.37), residues: 550 helix: 1.77 (0.30), residues: 297 sheet: -2.99 (0.54), residues: 72 loop : 0.15 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR A 86 PHE 0.013 0.001 PHE A 432 TRP 0.008 0.001 TRP A 160 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4335) covalent geometry : angle 0.57031 ( 5915) hydrogen bonds : bond 0.02841 ( 217) hydrogen bonds : angle 3.55747 ( 615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8380 (t0) cc_final: 0.8149 (t0) REVERT: A 143 ASP cc_start: 0.8943 (t0) cc_final: 0.8425 (t0) REVERT: A 154 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8501 (mm) REVERT: A 361 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8610 (p) REVERT: A 369 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7469 (pp) REVERT: A 373 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.5909 (mm) REVERT: A 415 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7937 (tt0) REVERT: A 424 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7279 (tt0) outliers start: 11 outliers final: 7 residues processed: 55 average time/residue: 0.0388 time to fit residues: 2.9849 Evaluate side-chains 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.150529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122467 restraints weight = 4894.004| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.43 r_work: 0.3179 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4335 Z= 0.127 Angle : 0.571 5.920 5915 Z= 0.257 Chirality : 0.042 0.247 714 Planarity : 0.004 0.048 762 Dihedral : 6.372 78.154 612 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.48 % Allowed : 13.54 % Favored : 83.97 % 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 are not related in a simple way. whole: 0.84 (0.37), residues: 550 helix: 1.80 (0.30), residues: 297 sheet: -2.91 (0.55), residues: 72 loop : 0.14 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR A 86 PHE 0.012 0.001 PHE A 432 TRP 0.007 0.001 TRP A 160 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4335) covalent geometry : angle 0.57144 ( 5915) hydrogen bonds : bond 0.02821 ( 217) hydrogen bonds : angle 3.51415 ( 615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8384 (t0) cc_final: 0.8148 (t0) REVERT: A 143 ASP cc_start: 0.8940 (t0) cc_final: 0.8392 (t0) REVERT: A 154 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8484 (mm) REVERT: A 274 ASP cc_start: 0.8355 (m-30) cc_final: 0.7996 (m-30) REVERT: A 361 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 369 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7452 (pp) REVERT: A 373 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.5904 (mm) REVERT: A 415 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7932 (tt0) REVERT: A 424 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7272 (tt0) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.0327 time to fit residues: 2.4638 Evaluate side-chains 57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123209 restraints weight = 4910.998| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.44 r_work: 0.3190 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4335 Z= 0.118 Angle : 0.566 5.896 5915 Z= 0.254 Chirality : 0.041 0.238 714 Planarity : 0.004 0.048 762 Dihedral : 6.333 77.114 612 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.26 % Allowed : 14.22 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.37), residues: 550 helix: 1.83 (0.30), residues: 297 sheet: -2.82 (0.56), residues: 72 loop : 0.14 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR A 86 PHE 0.012 0.001 PHE A 432 TRP 0.007 0.001 TRP A 160 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4335) covalent geometry : angle 0.56588 ( 5915) hydrogen bonds : bond 0.02746 ( 217) hydrogen bonds : angle 3.48238 ( 615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 911.12 seconds wall clock time: 16 minutes 22.30 seconds (982.30 seconds total)