Starting phenix.real_space_refine on Fri Aug 22 14:33:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2c_38850/08_2025/8y2c_38850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2c_38850/08_2025/8y2c_38850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y2c_38850/08_2025/8y2c_38850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2c_38850/08_2025/8y2c_38850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y2c_38850/08_2025/8y2c_38850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2c_38850/08_2025/8y2c_38850.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2805 2.51 5 N 660 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4207 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4179 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 505} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.14, per 1000 atoms: 0.27 Number of scatterers: 4207 At special positions: 0 Unit cell: (78.2, 68, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 719 8.00 N 660 7.00 C 2805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 188 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 175.2 milliseconds Enol-peptide restraints added in 1.4 microseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 76.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.508A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.875A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.656A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.627A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.777A pdb=" N GLN A 226 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 227 " --> pdb=" O LEU A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 237 through 256 removed outlier: 3.786A pdb=" N CYS A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.543A pdb=" N THR A 271 " --> pdb=" O TRP A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.732A pdb=" N ARG A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.707A pdb=" N ALA A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.709A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.581A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.506A pdb=" N VAL A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.579A pdb=" N TYR A 394 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.684A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 461 removed outlier: 3.808A pdb=" N PHE A 448 " --> pdb=" O HIS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.699A pdb=" N THR A 465 " --> pdb=" O PHE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 467 through 479 removed outlier: 3.957A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.906A pdb=" N PHE A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.653A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.568A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 600 through 605 removed outlier: 4.023A pdb=" N ASP A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 removed outlier: 3.528A pdb=" N TYR A 548 " --> pdb=" O TYR A 551 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 756 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: 0.64 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1253 1.34 - 1.46: 1127 1.46 - 1.58: 1923 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4337 Sorted by residual: bond pdb=" CB VAL A 495 " pdb=" CG1 VAL A 495 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.63e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C5 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" CG MET A 116 " pdb=" SD MET A 116 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB MET A 116 " pdb=" CG MET A 116 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.12e+00 ... (remaining 4332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 5841 1.84 - 3.67: 69 3.67 - 5.51: 9 5.51 - 7.35: 1 7.35 - 9.18: 1 Bond angle restraints: 5921 Sorted by residual: angle pdb=" C VAL A 495 " pdb=" CA VAL A 495 " pdb=" CB VAL A 495 " ideal model delta sigma weight residual 112.16 108.04 4.12 1.55e+00 4.16e-01 7.07e+00 angle pdb=" C PHE A 543 " pdb=" N ARG A 544 " pdb=" CA ARG A 544 " ideal model delta sigma weight residual 121.80 127.76 -5.96 2.44e+00 1.68e-01 5.97e+00 angle pdb=" CG MET A 116 " pdb=" SD MET A 116 " pdb=" CE MET A 116 " ideal model delta sigma weight residual 100.90 95.78 5.12 2.20e+00 2.07e-01 5.42e+00 angle pdb=" C TYR A 115 " pdb=" N MET A 116 " pdb=" CA MET A 116 " ideal model delta sigma weight residual 120.54 123.25 -2.71 1.35e+00 5.49e-01 4.03e+00 angle pdb=" C VAL A 495 " pdb=" N ALA A 496 " pdb=" CA ALA A 496 " ideal model delta sigma weight residual 121.81 118.31 3.50 1.83e+00 2.99e-01 3.66e+00 ... (remaining 5916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 2148 21.19 - 42.37: 264 42.37 - 63.56: 47 63.56 - 84.74: 10 84.74 - 105.92: 5 Dihedral angle restraints: 2474 sinusoidal: 950 harmonic: 1524 Sorted by residual: dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual 53.78 -52.14 105.92 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O4 NAG A 701 " ideal model delta sinusoidal sigma weight residual 175.11 70.28 104.83 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" C5 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sinusoidal sigma weight residual -174.13 -69.84 -104.29 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 2471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 457 0.034 - 0.068: 171 0.068 - 0.102: 35 0.102 - 0.136: 12 0.136 - 0.170: 2 Chirality restraints: 677 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 188 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CB ILE A 564 " pdb=" CA ILE A 564 " pdb=" CG1 ILE A 564 " pdb=" CG2 ILE A 564 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 674 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 394 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO A 395 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 106 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C MET A 106 " 0.027 2.00e-02 2.50e+03 pdb=" O MET A 106 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 107 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 494 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C GLY A 494 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY A 494 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL A 495 " -0.007 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 89 2.71 - 3.26: 4100 3.26 - 3.80: 6562 3.80 - 4.35: 7730 4.35 - 4.90: 13853 Nonbonded interactions: 32334 Sorted by model distance: nonbonded pdb=" OH TYR A 593 " pdb=" OD1 ASP A 605 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASN A 82 " pdb=" OG SER A 357 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" O ILE A 379 " model vdw 2.282 3.040 nonbonded pdb=" NH1 ARG A 125 " pdb=" O ASN A 336 " model vdw 2.293 3.120 nonbonded pdb=" O GLU A 126 " pdb=" OG SER A 334 " model vdw 2.300 3.040 ... (remaining 32329 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: 1.150 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.042 4340 Z= 0.131 Angle : 0.511 9.182 5929 Z= 0.257 Chirality : 0.038 0.170 677 Planarity : 0.004 0.054 723 Dihedral : 19.028 105.925 1497 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 34.68 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.38), residues: 523 helix: 1.36 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.64 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 606 TYR 0.017 0.001 TYR A 370 PHE 0.011 0.001 PHE A 155 TRP 0.013 0.001 TRP A 256 HIS 0.004 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4337) covalent geometry : angle 0.50921 ( 5921) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.79147 ( 2) hydrogen bonds : bond 0.11083 ( 253) hydrogen bonds : angle 4.21732 ( 756) link_NAG-ASN : bond 0.00228 ( 2) link_NAG-ASN : angle 1.42411 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.163 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0647 time to fit residues: 3.0834 Evaluate side-chains 34 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.150926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128475 restraints weight = 5446.157| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.99 r_work: 0.3376 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4340 Z= 0.222 Angle : 0.632 11.688 5929 Z= 0.311 Chirality : 0.043 0.202 677 Planarity : 0.005 0.061 723 Dihedral : 7.796 52.201 611 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.95 % Allowed : 31.53 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.37), residues: 523 helix: 1.11 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.81 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 544 TYR 0.014 0.002 TYR A 156 PHE 0.019 0.002 PHE A 412 TRP 0.020 0.002 TRP A 256 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 4337) covalent geometry : angle 0.62975 ( 5921) SS BOND : bond 0.00153 ( 1) SS BOND : angle 1.72341 ( 2) hydrogen bonds : bond 0.06034 ( 253) hydrogen bonds : angle 4.43221 ( 756) link_NAG-ASN : bond 0.00470 ( 2) link_NAG-ASN : angle 1.62280 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.144 Fit side-chains REVERT: A 92 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.7028 (mtpt) REVERT: A 105 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.6675 (t80) REVERT: A 307 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: A 544 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6631 (ptt-90) outliers start: 22 outliers final: 13 residues processed: 51 average time/residue: 0.0665 time to fit residues: 4.3901 Evaluate side-chains 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.155045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131380 restraints weight = 5269.574| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.17 r_work: 0.3211 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4340 Z= 0.110 Angle : 0.497 10.702 5929 Z= 0.245 Chirality : 0.038 0.165 677 Planarity : 0.004 0.054 723 Dihedral : 4.658 29.961 611 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.50 % Allowed : 31.98 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.38), residues: 523 helix: 1.35 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -1.74 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 85 TYR 0.008 0.001 TYR A 575 PHE 0.011 0.001 PHE A 155 TRP 0.009 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4337) covalent geometry : angle 0.49479 ( 5921) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.76685 ( 2) hydrogen bonds : bond 0.04320 ( 253) hydrogen bonds : angle 4.10665 ( 756) link_NAG-ASN : bond 0.00412 ( 2) link_NAG-ASN : angle 1.34730 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.150 Fit side-chains REVERT: A 544 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6402 (ptt-90) outliers start: 20 outliers final: 13 residues processed: 47 average time/residue: 0.0520 time to fit residues: 3.3474 Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7522 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.155480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131778 restraints weight = 5235.384| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.17 r_work: 0.3208 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4340 Z= 0.109 Angle : 0.481 8.856 5929 Z= 0.237 Chirality : 0.037 0.167 677 Planarity : 0.004 0.054 723 Dihedral : 4.200 26.824 611 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.50 % Allowed : 33.11 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.38), residues: 523 helix: 1.54 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.60 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.007 0.001 TYR A 575 PHE 0.011 0.001 PHE A 155 TRP 0.008 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4337) covalent geometry : angle 0.47829 ( 5921) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.78232 ( 2) hydrogen bonds : bond 0.04125 ( 253) hydrogen bonds : angle 4.04779 ( 756) link_NAG-ASN : bond 0.00377 ( 2) link_NAG-ASN : angle 1.55466 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.101 Fit side-chains REVERT: A 544 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6421 (ptt-90) outliers start: 20 outliers final: 13 residues processed: 49 average time/residue: 0.0637 time to fit residues: 4.1545 Evaluate side-chains 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.147891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123872 restraints weight = 5320.512| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.17 r_work: 0.3179 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4340 Z= 0.153 Angle : 0.531 10.095 5929 Z= 0.262 Chirality : 0.039 0.181 677 Planarity : 0.004 0.056 723 Dihedral : 4.370 29.458 611 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.95 % Allowed : 32.21 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.38), residues: 523 helix: 1.40 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.68 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.012 0.001 TYR A 115 PHE 0.016 0.001 PHE A 412 TRP 0.011 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4337) covalent geometry : angle 0.52795 ( 5921) SS BOND : bond 0.00081 ( 1) SS BOND : angle 1.15022 ( 2) hydrogen bonds : bond 0.04969 ( 253) hydrogen bonds : angle 4.17718 ( 756) link_NAG-ASN : bond 0.00429 ( 2) link_NAG-ASN : angle 1.86672 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.131 Fit side-chains REVERT: A 381 ASP cc_start: 0.8504 (t0) cc_final: 0.8035 (t0) REVERT: A 544 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6398 (ptt-90) REVERT: A 598 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7006 (mt-10) outliers start: 22 outliers final: 20 residues processed: 52 average time/residue: 0.0577 time to fit residues: 4.0310 Evaluate side-chains 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130877 restraints weight = 5334.907| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.16 r_work: 0.3266 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4340 Z= 0.103 Angle : 0.460 8.004 5929 Z= 0.228 Chirality : 0.037 0.158 677 Planarity : 0.004 0.053 723 Dihedral : 4.002 26.416 611 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.50 % Allowed : 32.66 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.38), residues: 523 helix: 1.59 (0.29), residues: 369 sheet: None (None), residues: 0 loop : -1.62 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.007 0.001 TYR A 115 PHE 0.010 0.001 PHE A 155 TRP 0.009 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 4337) covalent geometry : angle 0.45699 ( 5921) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.70948 ( 2) hydrogen bonds : bond 0.03968 ( 253) hydrogen bonds : angle 4.01555 ( 756) link_NAG-ASN : bond 0.00382 ( 2) link_NAG-ASN : angle 1.60553 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.130 Fit side-chains REVERT: A 116 MET cc_start: 0.8021 (ttp) cc_final: 0.7811 (ttt) REVERT: A 381 ASP cc_start: 0.8583 (t0) cc_final: 0.8023 (t0) REVERT: A 544 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6452 (ptt-90) outliers start: 20 outliers final: 15 residues processed: 52 average time/residue: 0.0545 time to fit residues: 3.7594 Evaluate side-chains 52 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.152151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128019 restraints weight = 5360.311| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.16 r_work: 0.3276 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4340 Z= 0.117 Angle : 0.477 8.957 5929 Z= 0.235 Chirality : 0.038 0.164 677 Planarity : 0.004 0.054 723 Dihedral : 4.023 26.081 611 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.95 % Allowed : 32.43 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.38), residues: 523 helix: 1.59 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.62 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.009 0.001 TYR A 115 PHE 0.012 0.001 PHE A 412 TRP 0.008 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4337) covalent geometry : angle 0.47431 ( 5921) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.85604 ( 2) hydrogen bonds : bond 0.04231 ( 253) hydrogen bonds : angle 4.02915 ( 756) link_NAG-ASN : bond 0.00374 ( 2) link_NAG-ASN : angle 1.62445 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.101 Fit side-chains REVERT: A 381 ASP cc_start: 0.8614 (t0) cc_final: 0.8039 (t0) REVERT: A 544 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6475 (ptt-90) outliers start: 22 outliers final: 18 residues processed: 53 average time/residue: 0.0503 time to fit residues: 3.5761 Evaluate side-chains 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.155237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131643 restraints weight = 5223.320| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.12 r_work: 0.3228 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4340 Z= 0.110 Angle : 0.488 10.418 5929 Z= 0.238 Chirality : 0.038 0.161 677 Planarity : 0.004 0.053 723 Dihedral : 3.928 25.068 611 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.73 % Allowed : 33.11 % Favored : 62.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.38), residues: 523 helix: 1.49 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.52 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.008 0.001 TYR A 370 PHE 0.011 0.001 PHE A 155 TRP 0.008 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4337) covalent geometry : angle 0.48588 ( 5921) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.74381 ( 2) hydrogen bonds : bond 0.04087 ( 253) hydrogen bonds : angle 4.08341 ( 756) link_NAG-ASN : bond 0.00373 ( 2) link_NAG-ASN : angle 1.57810 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.118 Fit side-chains REVERT: A 381 ASP cc_start: 0.8583 (t0) cc_final: 0.7888 (t0) REVERT: A 544 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6428 (ptt-90) outliers start: 21 outliers final: 18 residues processed: 53 average time/residue: 0.0524 time to fit residues: 3.7945 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 0.0000 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.151670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127583 restraints weight = 5330.577| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.15 r_work: 0.3205 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4340 Z= 0.132 Angle : 0.517 10.556 5929 Z= 0.252 Chirality : 0.039 0.169 677 Planarity : 0.004 0.054 723 Dihedral : 4.064 26.581 611 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.73 % Allowed : 33.33 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.38), residues: 523 helix: 1.51 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.62 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.009 0.001 TYR A 88 PHE 0.014 0.001 PHE A 412 TRP 0.009 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4337) covalent geometry : angle 0.51466 ( 5921) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.97377 ( 2) hydrogen bonds : bond 0.04508 ( 253) hydrogen bonds : angle 4.12353 ( 756) link_NAG-ASN : bond 0.00386 ( 2) link_NAG-ASN : angle 1.67780 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.170 Fit side-chains REVERT: A 164 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7456 (tp) REVERT: A 381 ASP cc_start: 0.8578 (t0) cc_final: 0.7946 (t0) REVERT: A 544 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6420 (ptt-90) outliers start: 21 outliers final: 18 residues processed: 52 average time/residue: 0.0531 time to fit residues: 3.6772 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 28 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.156699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132953 restraints weight = 5190.784| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.11 r_work: 0.3292 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4340 Z= 0.095 Angle : 0.465 9.027 5929 Z= 0.228 Chirality : 0.037 0.149 677 Planarity : 0.004 0.052 723 Dihedral : 3.758 23.039 611 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.05 % Allowed : 33.78 % Favored : 62.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.39), residues: 523 helix: 1.57 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.44 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.010 0.001 TYR A 370 PHE 0.012 0.001 PHE A 155 TRP 0.010 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 4337) covalent geometry : angle 0.46298 ( 5921) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.56876 ( 2) hydrogen bonds : bond 0.03658 ( 253) hydrogen bonds : angle 3.98491 ( 756) link_NAG-ASN : bond 0.00378 ( 2) link_NAG-ASN : angle 1.45875 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.142 Fit side-chains REVERT: A 381 ASP cc_start: 0.8484 (t0) cc_final: 0.7883 (t0) REVERT: A 544 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6429 (ptt-90) outliers start: 18 outliers final: 15 residues processed: 52 average time/residue: 0.0490 time to fit residues: 3.4460 Evaluate side-chains 54 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.0270 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.0060 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.156844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132702 restraints weight = 5270.417| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.17 r_work: 0.3271 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4340 Z= 0.094 Angle : 0.446 8.039 5929 Z= 0.220 Chirality : 0.037 0.148 677 Planarity : 0.004 0.053 723 Dihedral : 3.659 21.141 611 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.05 % Allowed : 33.33 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.39), residues: 523 helix: 1.64 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.38 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 544 TYR 0.008 0.001 TYR A 370 PHE 0.010 0.001 PHE A 155 TRP 0.009 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 4337) covalent geometry : angle 0.44403 ( 5921) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.58588 ( 2) hydrogen bonds : bond 0.03552 ( 253) hydrogen bonds : angle 3.92923 ( 756) link_NAG-ASN : bond 0.00359 ( 2) link_NAG-ASN : angle 1.39758 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1002.88 seconds wall clock time: 17 minutes 57.23 seconds (1077.23 seconds total)