Starting phenix.real_space_refine on Tue Feb 3 15:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kts_62564/02_2026/9kts_62564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kts_62564/02_2026/9kts_62564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kts_62564/02_2026/9kts_62564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kts_62564/02_2026/9kts_62564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kts_62564/02_2026/9kts_62564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kts_62564/02_2026/9kts_62564.map" } resolution = 3.2 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 2820 2.51 5 N 644 2.21 5 O 731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 4228 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4218 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 27, 'TRANS': 509} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1, 'water': 9} Link IDs: {None: 9} Time building chain proxies: 0.71, per 1000 atoms: 0.17 Number of scatterers: 4228 At special positions: 0 Unit cell: (82.41, 69.68, 81.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 32 16.00 O 731 8.00 N 644 7.00 C 2820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 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: 0.22 Conformation dependent library (CDL) restraints added in 98.2 milliseconds 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.504A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.406A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 152 removed outlier: 3.841A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.403A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 236 Processing helix chain 'A' and resid 244 through 267 removed outlier: 3.785A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.878A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.195A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.718A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.015A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.758A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.667A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 removed outlier: 4.093A pdb=" N PHE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.102A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.914A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.512A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.402A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.658A pdb=" N PHE A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.921A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 272 hydrogen bonds defined for protein. 795 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: 0.41 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1239 1.35 - 1.46: 1241 1.46 - 1.58: 1829 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 4355 Sorted by residual: bond pdb=" C VAL A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.87e+00 bond pdb=" CA VAL A 239 " pdb=" CB VAL A 239 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.26e-01 bond pdb=" C PHE A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.20e-01 bond pdb=" CA THR A 242 " pdb=" CB THR A 242 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.86e-02 2.89e+03 2.79e-01 bond pdb=" N TYR A 418 " pdb=" CA TYR A 418 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.41e-02 5.03e+03 2.70e-01 ... (remaining 4350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 5903 2.05 - 4.10: 36 4.10 - 6.15: 8 6.15 - 8.20: 0 8.20 - 10.26: 1 Bond angle restraints: 5948 Sorted by residual: angle pdb=" C THR A 242 " pdb=" CA THR A 242 " pdb=" CB THR A 242 " ideal model delta sigma weight residual 116.54 110.98 5.56 1.15e+00 7.56e-01 2.34e+01 angle pdb=" CA LEU A 573 " pdb=" CB LEU A 573 " pdb=" CG LEU A 573 " ideal model delta sigma weight residual 116.30 126.56 -10.26 3.50e+00 8.16e-02 8.59e+00 angle pdb=" CA THR A 242 " pdb=" C THR A 242 " pdb=" N GLY A 243 " ideal model delta sigma weight residual 119.52 117.27 2.25 7.90e-01 1.60e+00 8.11e+00 angle pdb=" C ASN A 533 " pdb=" N LYS A 534 " pdb=" CA LYS A 534 " ideal model delta sigma weight residual 122.08 125.34 -3.26 1.47e+00 4.63e-01 4.93e+00 angle pdb=" CA TRP A 470 " pdb=" CB TRP A 470 " pdb=" CG TRP A 470 " ideal model delta sigma weight residual 113.60 116.74 -3.14 1.90e+00 2.77e-01 2.74e+00 ... (remaining 5943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2351 16.15 - 32.29: 90 32.29 - 48.43: 9 48.43 - 64.58: 4 64.58 - 80.72: 1 Dihedral angle restraints: 2455 sinusoidal: 910 harmonic: 1545 Sorted by residual: dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual 180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" N TYR A 69 " pdb=" CA TYR A 69 " pdb=" CB TYR A 69 " pdb=" CG TYR A 69 " ideal model delta sinusoidal sigma weight residual 60.00 116.35 -56.35 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" N LEU A 395 " pdb=" CA LEU A 395 " pdb=" CB LEU A 395 " pdb=" CG LEU A 395 " ideal model delta sinusoidal sigma weight residual -180.00 -125.44 -54.56 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 2452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 436 0.032 - 0.064: 166 0.064 - 0.096: 38 0.096 - 0.128: 18 0.128 - 0.161: 1 Chirality restraints: 659 Sorted by residual: chirality pdb=" CG LEU A 573 " pdb=" CB LEU A 573 " pdb=" CD1 LEU A 573 " pdb=" CD2 LEU A 573 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL A 528 " pdb=" N VAL A 528 " pdb=" C VAL A 528 " pdb=" CB VAL A 528 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA THR A 512 " pdb=" N THR A 512 " pdb=" C THR A 512 " pdb=" CB THR A 512 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 656 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 93 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO A 208 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 144 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C TRP A 144 " 0.018 2.00e-02 2.50e+03 pdb=" O TRP A 144 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA A 145 " -0.006 2.00e-02 2.50e+03 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1124 2.80 - 3.33: 4311 3.33 - 3.85: 7244 3.85 - 4.38: 8368 4.38 - 4.90: 14714 Nonbonded interactions: 35761 Sorted by model distance: nonbonded pdb=" O SER A 311 " pdb=" OG SER A 314 " model vdw 2.278 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.280 3.120 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.324 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.336 3.120 nonbonded pdb=" NE2 GLN A 289 " pdb=" OD1 ASP A 293 " model vdw 2.352 3.120 ... (remaining 35756 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: 3.840 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.790 Find NCS groups from input model: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.002 0.019 4356 Z= 0.096 Angle : 0.459 10.256 5950 Z= 0.249 Chirality : 0.038 0.161 659 Planarity : 0.003 0.027 729 Dihedral : 9.071 80.723 1474 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.25 % Allowed : 3.37 % Favored : 94.38 % 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: 0.72 (0.38), residues: 533 helix: 1.11 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.94 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 575 TYR 0.012 0.001 TYR A 69 PHE 0.010 0.001 PHE A 386 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00179 ( 4355) covalent geometry : angle 0.45893 ( 5948) SS BOND : bond 0.00285 ( 1) SS BOND : angle 1.02004 ( 2) hydrogen bonds : bond 0.16923 ( 272) hydrogen bonds : angle 7.47981 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.162 Fit side-chains REVERT: A 233 PHE cc_start: 0.6535 (m-10) cc_final: 0.6165 (m-80) REVERT: A 359 ILE cc_start: 0.8507 (mt) cc_final: 0.8268 (mt) REVERT: A 395 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8434 (mp) outliers start: 10 outliers final: 2 residues processed: 96 average time/residue: 0.0780 time to fit residues: 9.5169 Evaluate side-chains 67 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 212 HIS A 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.146059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.128071 restraints weight = 4998.445| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.65 r_work: 0.3303 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4356 Z= 0.134 Angle : 0.498 5.902 5950 Z= 0.260 Chirality : 0.040 0.135 659 Planarity : 0.004 0.034 729 Dihedral : 4.896 56.466 587 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.25 % Allowed : 8.54 % Favored : 89.21 % 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: 1.10 (0.37), residues: 533 helix: 1.45 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.09 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 427 TYR 0.017 0.001 TYR A 69 PHE 0.023 0.001 PHE A 404 TRP 0.012 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4355) covalent geometry : angle 0.49668 ( 5948) SS BOND : bond 0.00470 ( 1) SS BOND : angle 1.99218 ( 2) hydrogen bonds : bond 0.04043 ( 272) hydrogen bonds : angle 4.91919 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.165 Fit side-chains REVERT: A 207 SER cc_start: 0.8610 (m) cc_final: 0.8090 (p) REVERT: A 233 PHE cc_start: 0.6927 (m-10) cc_final: 0.6609 (m-80) REVERT: A 258 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8423 (tt) REVERT: A 328 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.6783 (mp) REVERT: A 359 ILE cc_start: 0.8595 (mt) cc_final: 0.8280 (mt) REVERT: A 581 THR cc_start: 0.8329 (m) cc_final: 0.8096 (p) outliers start: 10 outliers final: 5 residues processed: 77 average time/residue: 0.0495 time to fit residues: 5.0919 Evaluate side-chains 70 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.146759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.128678 restraints weight = 4948.349| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.62 r_work: 0.3294 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4356 Z= 0.134 Angle : 0.490 6.850 5950 Z= 0.252 Chirality : 0.040 0.128 659 Planarity : 0.004 0.032 729 Dihedral : 4.523 54.773 585 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.82 % Allowed : 8.54 % Favored : 87.64 % 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: 1.25 (0.37), residues: 533 helix: 1.55 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.92 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 427 TYR 0.018 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4355) covalent geometry : angle 0.48952 ( 5948) SS BOND : bond 0.00403 ( 1) SS BOND : angle 1.64395 ( 2) hydrogen bonds : bond 0.03843 ( 272) hydrogen bonds : angle 4.65970 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 207 SER cc_start: 0.8585 (m) cc_final: 0.8062 (p) REVERT: A 258 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8483 (tt) REVERT: A 328 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.6929 (mt) REVERT: A 359 ILE cc_start: 0.8565 (mt) cc_final: 0.8262 (mt) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.0436 time to fit residues: 4.9723 Evaluate side-chains 80 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 170 HIS A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.146356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.129026 restraints weight = 4950.938| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.53 r_work: 0.3294 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4356 Z= 0.119 Angle : 0.482 7.155 5950 Z= 0.247 Chirality : 0.039 0.126 659 Planarity : 0.004 0.032 729 Dihedral : 4.499 54.713 585 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.15 % Allowed : 10.11 % Favored : 86.74 % 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: 1.32 (0.37), residues: 533 helix: 1.62 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.99 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.017 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4355) covalent geometry : angle 0.48152 ( 5948) SS BOND : bond 0.00348 ( 1) SS BOND : angle 1.53398 ( 2) hydrogen bonds : bond 0.03604 ( 272) hydrogen bonds : angle 4.52921 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.148 Fit side-chains REVERT: A 207 SER cc_start: 0.8545 (m) cc_final: 0.8044 (p) REVERT: A 258 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8501 (tt) REVERT: A 328 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.6890 (mp) REVERT: A 359 ILE cc_start: 0.8579 (mt) cc_final: 0.8258 (mt) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 0.0505 time to fit residues: 5.3644 Evaluate side-chains 76 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.143072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.125658 restraints weight = 4990.051| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.56 r_work: 0.3230 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4356 Z= 0.135 Angle : 0.492 7.684 5950 Z= 0.253 Chirality : 0.040 0.128 659 Planarity : 0.004 0.033 729 Dihedral : 4.581 54.568 585 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.04 % Allowed : 8.76 % Favored : 87.19 % 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: 1.28 (0.37), residues: 533 helix: 1.61 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.03 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 427 TYR 0.018 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4355) covalent geometry : angle 0.49088 ( 5948) SS BOND : bond 0.00417 ( 1) SS BOND : angle 1.54208 ( 2) hydrogen bonds : bond 0.03716 ( 272) hydrogen bonds : angle 4.52940 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.154 Fit side-chains REVERT: A 207 SER cc_start: 0.8584 (m) cc_final: 0.8056 (p) REVERT: A 328 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.6849 (mp) outliers start: 18 outliers final: 15 residues processed: 79 average time/residue: 0.0493 time to fit residues: 5.4380 Evaluate side-chains 80 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.142821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125441 restraints weight = 5104.481| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.55 r_work: 0.3258 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4356 Z= 0.137 Angle : 0.493 7.685 5950 Z= 0.255 Chirality : 0.040 0.128 659 Planarity : 0.004 0.034 729 Dihedral : 4.613 54.387 585 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.27 % Allowed : 8.31 % Favored : 87.42 % 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: 1.25 (0.37), residues: 533 helix: 1.60 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.07 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 427 TYR 0.018 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4355) covalent geometry : angle 0.49206 ( 5948) SS BOND : bond 0.00410 ( 1) SS BOND : angle 1.53321 ( 2) hydrogen bonds : bond 0.03722 ( 272) hydrogen bonds : angle 4.52505 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.190 Fit side-chains REVERT: A 207 SER cc_start: 0.8551 (m) cc_final: 0.8038 (p) REVERT: A 258 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 328 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.6913 (mp) outliers start: 19 outliers final: 15 residues processed: 79 average time/residue: 0.0478 time to fit residues: 5.1554 Evaluate side-chains 80 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 0.0070 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.144978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.127635 restraints weight = 5065.084| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.56 r_work: 0.3252 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4356 Z= 0.114 Angle : 0.474 7.679 5950 Z= 0.244 Chirality : 0.039 0.124 659 Planarity : 0.004 0.034 729 Dihedral : 4.521 54.451 585 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.04 % Allowed : 8.54 % Favored : 87.42 % 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: 1.38 (0.37), residues: 533 helix: 1.70 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.016 0.001 TYR A 69 PHE 0.013 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4355) covalent geometry : angle 0.47348 ( 5948) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.40603 ( 2) hydrogen bonds : bond 0.03493 ( 272) hydrogen bonds : angle 4.41291 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.157 Fit side-chains REVERT: A 207 SER cc_start: 0.8575 (m) cc_final: 0.8074 (p) REVERT: A 258 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8437 (tt) REVERT: A 328 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.6884 (mp) REVERT: A 586 ASN cc_start: 0.6672 (p0) cc_final: 0.6420 (p0) outliers start: 18 outliers final: 16 residues processed: 78 average time/residue: 0.0529 time to fit residues: 5.7115 Evaluate side-chains 80 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.145616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128036 restraints weight = 4971.124| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.60 r_work: 0.3247 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4356 Z= 0.112 Angle : 0.473 7.630 5950 Z= 0.243 Chirality : 0.039 0.125 659 Planarity : 0.004 0.034 729 Dihedral : 4.494 54.494 585 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.27 % Allowed : 9.44 % Favored : 86.29 % 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: 1.41 (0.37), residues: 533 helix: 1.73 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.06 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 428 TYR 0.016 0.001 TYR A 69 PHE 0.013 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4355) covalent geometry : angle 0.47254 ( 5948) SS BOND : bond 0.00305 ( 1) SS BOND : angle 1.34599 ( 2) hydrogen bonds : bond 0.03490 ( 272) hydrogen bonds : angle 4.37450 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.157 Fit side-chains REVERT: A 207 SER cc_start: 0.8614 (m) cc_final: 0.8105 (p) REVERT: A 258 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 328 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6804 (mp) REVERT: A 586 ASN cc_start: 0.6330 (p0) cc_final: 0.6106 (p0) outliers start: 19 outliers final: 16 residues processed: 79 average time/residue: 0.0660 time to fit residues: 6.8173 Evaluate side-chains 81 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.0170 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.143225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.125888 restraints weight = 5099.183| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.55 r_work: 0.3245 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4356 Z= 0.128 Angle : 0.494 7.568 5950 Z= 0.253 Chirality : 0.040 0.126 659 Planarity : 0.004 0.034 729 Dihedral : 4.551 54.357 585 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.49 % Allowed : 9.21 % Favored : 86.29 % 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: 1.30 (0.37), residues: 533 helix: 1.65 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.11 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.017 0.001 TYR A 69 PHE 0.015 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4355) covalent geometry : angle 0.49332 ( 5948) SS BOND : bond 0.00328 ( 1) SS BOND : angle 1.45290 ( 2) hydrogen bonds : bond 0.03616 ( 272) hydrogen bonds : angle 4.43525 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.153 Fit side-chains REVERT: A 207 SER cc_start: 0.8558 (m) cc_final: 0.8075 (p) REVERT: A 258 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8464 (tt) REVERT: A 328 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.6926 (mp) REVERT: A 586 ASN cc_start: 0.6362 (p0) cc_final: 0.6077 (p0) outliers start: 20 outliers final: 16 residues processed: 77 average time/residue: 0.0568 time to fit residues: 5.8791 Evaluate side-chains 77 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 47 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.144795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126871 restraints weight = 4986.540| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.63 r_work: 0.3286 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4356 Z= 0.117 Angle : 0.492 7.599 5950 Z= 0.252 Chirality : 0.040 0.159 659 Planarity : 0.004 0.034 729 Dihedral : 4.510 54.304 585 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.04 % Allowed : 9.21 % Favored : 86.74 % 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: 1.33 (0.37), residues: 533 helix: 1.67 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.08 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 240 TYR 0.016 0.001 TYR A 69 PHE 0.013 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4355) covalent geometry : angle 0.49113 ( 5948) SS BOND : bond 0.00282 ( 1) SS BOND : angle 1.29817 ( 2) hydrogen bonds : bond 0.03524 ( 272) hydrogen bonds : angle 4.40098 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.149 Fit side-chains REVERT: A 207 SER cc_start: 0.8582 (m) cc_final: 0.8081 (p) REVERT: A 258 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8434 (tt) REVERT: A 328 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.6882 (mp) outliers start: 18 outliers final: 16 residues processed: 74 average time/residue: 0.0435 time to fit residues: 4.4273 Evaluate side-chains 78 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.143106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125227 restraints weight = 5048.987| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.64 r_work: 0.3216 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4356 Z= 0.132 Angle : 0.503 7.547 5950 Z= 0.260 Chirality : 0.040 0.149 659 Planarity : 0.004 0.034 729 Dihedral : 4.577 54.229 585 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.49 % Allowed : 9.44 % Favored : 86.07 % 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: 1.27 (0.37), residues: 533 helix: 1.62 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -1.09 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.018 0.001 TYR A 69 PHE 0.015 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4355) covalent geometry : angle 0.50257 ( 5948) SS BOND : bond 0.00385 ( 1) SS BOND : angle 1.41996 ( 2) hydrogen bonds : bond 0.03664 ( 272) hydrogen bonds : angle 4.45145 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1085.60 seconds wall clock time: 19 minutes 19.26 seconds (1159.26 seconds total)