Starting phenix.real_space_refine on Wed Jul 1 23:45:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jcz_61378/07_2026/9jcz_61378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jcz_61378/07_2026/9jcz_61378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jcz_61378/07_2026/9jcz_61378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jcz_61378/07_2026/9jcz_61378.map" model { file = "/net/cci-nas-00/data/ceres_data/9jcz_61378/07_2026/9jcz_61378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jcz_61378/07_2026/9jcz_61378.cif" } resolution = 2.64 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= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2945 2.51 5 N 638 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4364 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 525, 4164 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 525, 4164 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4293 Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 191 Ad-hoc single atom residues: {' NA': 2, ' CL': 1} Unusual residues: {'NAG': 3, 'TAU': 1, 'Y01': 4} Classifications: {'undetermined': 8, 'water': 2} Link IDs: {None: 8} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 301 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 301 " occ=0.50 Time building chain proxies: 1.39, per 1000 atoms: 0.32 Number of scatterers: 4364 At special positions: 0 Unit cell: (73.628, 68.968, 85.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 745 8.00 N 638 7.00 C 2945 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 179 " " NAG A 702 " - " ASN A 190 " " NAG A 710 " - " ASN A 163 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 171.8 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 958 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.876A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.848A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 4.025A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 106 removed outlier: 6.348A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.654A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 152 removed outlier: 3.862A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (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 237 Processing helix chain 'A' and resid 244 through 267 removed outlier: 4.166A 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: 3.810A 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 302 removed outlier: 4.101A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.836A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.302A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.507A pdb=" N ASP A 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 362' Processing helix chain 'A' and resid 369 through 381 Proline residue: A 375 - end of helix removed outlier: 3.604A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.602A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 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: 4.278A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.638A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.607A pdb=" N LEU A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.860A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 260 hydrogen bonds defined for protein. 762 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: 0.39 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 653 1.32 - 1.45: 1328 1.45 - 1.57: 2479 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 4507 Sorted by residual: bond pdb=" N ARG A 41 " pdb=" CA ARG A 41 " ideal model delta sigma weight residual 1.456 1.414 0.042 1.22e-02 6.72e+03 1.19e+01 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" CAX Y01 A 707 " pdb=" OAF Y01 A 707 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" CAX Y01 A 708 " pdb=" OAH Y01 A 708 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" CAX Y01 A 706 " pdb=" OAF Y01 A 706 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 9.03e+00 ... (remaining 4502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 6128 3.54 - 7.08: 29 7.08 - 10.62: 7 10.62 - 14.16: 1 14.16 - 17.70: 1 Bond angle restraints: 6166 Sorted by residual: angle pdb=" O1 TAU A 711 " pdb=" S TAU A 711 " pdb=" O2 TAU A 711 " ideal model delta sigma weight residual 113.04 95.34 17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" N VAL A 362 " pdb=" CA VAL A 362 " pdb=" C VAL A 362 " ideal model delta sigma weight residual 113.47 109.60 3.87 1.01e+00 9.80e-01 1.47e+01 angle pdb=" C2 TAU A 711 " pdb=" S TAU A 711 " pdb=" O2 TAU A 711 " ideal model delta sigma weight residual 105.35 116.37 -11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ARG A 41 " pdb=" CA ARG A 41 " pdb=" CB ARG A 41 " ideal model delta sigma weight residual 109.85 104.57 5.28 1.49e+00 4.50e-01 1.26e+01 angle pdb=" C ASN A 167 " pdb=" N THR A 168 " pdb=" CA THR A 168 " ideal model delta sigma weight residual 120.68 125.66 -4.98 1.52e+00 4.33e-01 1.07e+01 ... (remaining 6161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.02: 2643 25.02 - 50.05: 110 50.05 - 75.07: 16 75.07 - 100.10: 6 100.10 - 125.12: 4 Dihedral angle restraints: 2779 sinusoidal: 1264 harmonic: 1515 Sorted by residual: dihedral pdb=" C2 NAG A 702 " pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " pdb=" C5 NAG A 702 " ideal model delta sinusoidal sigma weight residual -62.96 62.16 -125.12 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CBC Y01 A 708 " pdb=" CAR Y01 A 708 " pdb=" CAT Y01 A 708 " pdb=" CBH Y01 A 708 " ideal model delta sinusoidal sigma weight residual -57.13 63.88 -121.01 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" CAT Y01 A 708 " pdb=" CAR Y01 A 708 " pdb=" CBC Y01 A 708 " pdb=" OAW Y01 A 708 " ideal model delta sinusoidal sigma weight residual 178.96 68.04 110.92 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 2776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 588 0.056 - 0.111: 95 0.111 - 0.167: 9 0.167 - 0.223: 1 0.223 - 0.278: 1 Chirality restraints: 694 Sorted by residual: chirality pdb=" CA ASP A 401 " pdb=" N ASP A 401 " pdb=" C ASP A 401 " pdb=" CB ASP A 401 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CBB Y01 A 709 " pdb=" CAC Y01 A 709 " pdb=" CAO Y01 A 709 " pdb=" CBE Y01 A 709 " both_signs ideal model delta sigma weight residual False 2.58 2.41 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA LEU A 400 " pdb=" N LEU A 400 " pdb=" C LEU A 400 " pdb=" CB LEU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 691 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASER A 301 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C ASER A 301 " 0.052 2.00e-02 2.50e+03 pdb=" O ASER A 301 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 302 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BSER A 301 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C BSER A 301 " -0.048 2.00e-02 2.50e+03 pdb=" O BSER A 301 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR A 302 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 296 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C THR A 296 " 0.040 2.00e-02 2.50e+03 pdb=" O THR A 296 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 297 " -0.014 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 26 2.50 - 3.10: 3153 3.10 - 3.70: 6470 3.70 - 4.30: 9447 4.30 - 4.90: 16023 Nonbonded interactions: 35119 Sorted by model distance: nonbonded pdb=" O VAL A 59 " pdb="NA NA A 703 " model vdw 1.897 3.210 nonbonded pdb=" OD1 ASN A 63 " pdb="NA NA A 704 " model vdw 1.931 3.210 nonbonded pdb=" OG ASER A 301 " pdb="NA NA A 704 " model vdw 1.947 3.210 nonbonded pdb=" OD1 ASP A 401 " pdb="NA NA A 703 " model vdw 1.955 3.210 nonbonded pdb=" O GLY A 56 " pdb="NA NA A 703 " model vdw 1.964 3.210 ... (remaining 35114 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=0.50 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: 0.770 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: 4.900 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.004 0.065 4511 Z= 0.230 Angle : 0.751 17.702 6177 Z= 0.380 Chirality : 0.042 0.278 694 Planarity : 0.004 0.042 725 Dihedral : 14.872 125.121 1818 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.88 (0.38), residues: 524 helix: 1.45 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.17 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 41 TYR 0.012 0.001 TYR A 527 PHE 0.012 0.001 PHE A 391 TRP 0.019 0.001 TRP A 166 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.23 ( 4507) covalent geometry : angle 0.75017 / 0.38 ( 6166) SS BOND : bond 0.00166 / 0.11 ( 1) SS BOND : angle 0.99631 / 0.65 ( 2) hydrogen bonds : bond 0.14296 / 9.42 ( 260) hydrogen bonds : angle 5.08528 / 3.58 ( 762) link_NAG-ASN : bond 0.00385 / 0.20 ( 3) link_NAG-ASN : angle 0.98462 / 0.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.154 Fit side-chains REVERT: A 353 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6866 (tm-30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3808 time to fit residues: 26.3404 Evaluate side-chains 48 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 10.0000 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.163438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132615 restraints weight = 8374.216| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.59 r_work: 0.3618 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4511 Z= 0.128 Angle : 0.608 12.818 6177 Z= 0.298 Chirality : 0.041 0.186 694 Planarity : 0.004 0.042 725 Dihedral : 12.108 112.878 919 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.89 % Allowed : 10.29 % Favored : 88.81 % 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: 1.12 (0.38), residues: 524 helix: 1.71 (0.29), residues: 351 sheet: None (None), residues: 0 loop : -1.33 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.013 0.001 TYR A 527 PHE 0.027 0.002 PHE A 50 TRP 0.020 0.001 TRP A 166 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 4507) covalent geometry : angle 0.60560 / 0.30 ( 6166) SS BOND : bond 0.00279 / 0.19 ( 1) SS BOND : angle 1.21368 / 0.78 ( 2) hydrogen bonds : bond 0.04578 / 2.99 ( 260) hydrogen bonds : angle 4.30296 / 2.94 ( 762) link_NAG-ASN : bond 0.00302 / 0.18 ( 3) link_NAG-ASN : angle 1.49758 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.160 Fit side-chains REVERT: A 324 ARG cc_start: 0.5955 (mmm160) cc_final: 0.5672 (mmm160) REVERT: A 353 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6756 (tm-30) REVERT: A 394 MET cc_start: 0.8516 (ttp) cc_final: 0.8309 (ttp) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.3900 time to fit residues: 20.8893 Evaluate side-chains 46 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.160827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129246 restraints weight = 9867.211| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.80 r_work: 0.3572 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4511 Z= 0.132 Angle : 0.619 11.598 6177 Z= 0.301 Chirality : 0.043 0.188 694 Planarity : 0.004 0.047 725 Dihedral : 10.289 105.434 919 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.67 % Allowed : 12.98 % Favored : 86.35 % 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: 1.02 (0.38), residues: 524 helix: 1.58 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.015 0.001 TYR A 489 PHE 0.025 0.002 PHE A 391 TRP 0.023 0.001 TRP A 166 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4507) covalent geometry : angle 0.61691 / 0.30 ( 6166) SS BOND : bond 0.00337 / 0.22 ( 1) SS BOND : angle 1.11603 / 0.72 ( 2) hydrogen bonds : bond 0.04518 / 2.96 ( 260) hydrogen bonds : angle 4.25793 / 2.90 ( 762) link_NAG-ASN : bond 0.00268 / 0.16 ( 3) link_NAG-ASN : angle 1.51613 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 297 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7570 (tp40) REVERT: A 353 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6823 (tm-30) REVERT: A 394 MET cc_start: 0.8541 (ttp) cc_final: 0.8281 (ttp) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.4145 time to fit residues: 21.4108 Evaluate side-chains 45 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129131 restraints weight = 10843.920| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.93 r_work: 0.3566 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4511 Z= 0.122 Angle : 0.590 10.586 6177 Z= 0.289 Chirality : 0.042 0.192 694 Planarity : 0.004 0.047 725 Dihedral : 9.925 104.339 919 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.34 % Allowed : 13.42 % Favored : 85.23 % 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: 1.11 (0.38), residues: 524 helix: 1.67 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.35 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.010 0.001 TYR A 489 PHE 0.027 0.002 PHE A 434 TRP 0.026 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 4507) covalent geometry : angle 0.58719 / 0.29 ( 6166) SS BOND : bond 0.00363 / 0.24 ( 1) SS BOND : angle 1.21371 / 0.78 ( 2) hydrogen bonds : bond 0.04328 / 2.83 ( 260) hydrogen bonds : angle 4.22474 / 2.89 ( 762) link_NAG-ASN : bond 0.00283 / 0.16 ( 3) link_NAG-ASN : angle 1.50442 / 0.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 353 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 394 MET cc_start: 0.8496 (ttp) cc_final: 0.8168 (ttp) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.4143 time to fit residues: 20.9272 Evaluate side-chains 44 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.157999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123293 restraints weight = 15863.774| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.84 r_work: 0.3453 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4511 Z= 0.118 Angle : 0.569 9.712 6177 Z= 0.280 Chirality : 0.041 0.194 694 Planarity : 0.004 0.048 725 Dihedral : 9.675 101.555 919 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.12 % Allowed : 14.54 % Favored : 84.34 % 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: 1.12 (0.38), residues: 524 helix: 1.65 (0.28), residues: 361 sheet: None (None), residues: 0 loop : -1.35 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.013 0.001 TYR A 69 PHE 0.026 0.002 PHE A 391 TRP 0.027 0.001 TRP A 166 HIS 0.001 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 4507) covalent geometry : angle 0.56632 / 0.28 ( 6166) SS BOND : bond 0.00389 / 0.26 ( 1) SS BOND : angle 1.12099 / 0.72 ( 2) hydrogen bonds : bond 0.04229 / 2.77 ( 260) hydrogen bonds : angle 4.19787 / 2.87 ( 762) link_NAG-ASN : bond 0.00292 / 0.17 ( 3) link_NAG-ASN : angle 1.51745 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.153 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 0.3088 time to fit residues: 15.4373 Evaluate side-chains 44 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 0.0050 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.159532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126833 restraints weight = 9240.204| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.98 r_work: 0.3522 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4511 Z= 0.110 Angle : 0.560 9.163 6177 Z= 0.274 Chirality : 0.041 0.194 694 Planarity : 0.004 0.047 725 Dihedral : 9.541 99.379 919 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.12 % Allowed : 14.54 % Favored : 84.34 % 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: 1.19 (0.38), residues: 524 helix: 1.79 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.47 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.012 0.001 TYR A 69 PHE 0.030 0.002 PHE A 434 TRP 0.032 0.001 TRP A 166 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 4507) covalent geometry : angle 0.55668 / 0.27 ( 6166) SS BOND : bond 0.00346 / 0.23 ( 1) SS BOND : angle 1.04604 / 0.68 ( 2) hydrogen bonds : bond 0.03894 / 2.55 ( 260) hydrogen bonds : angle 4.14413 / 2.82 ( 762) link_NAG-ASN : bond 0.00285 / 0.17 ( 3) link_NAG-ASN : angle 1.51974 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.108 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.3674 time to fit residues: 17.3931 Evaluate side-chains 43 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.158175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124470 restraints weight = 10817.286| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.26 r_work: 0.3485 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4511 Z= 0.116 Angle : 0.568 8.766 6177 Z= 0.279 Chirality : 0.041 0.195 694 Planarity : 0.004 0.047 725 Dihedral : 9.471 97.853 919 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.67 % Allowed : 15.44 % Favored : 83.89 % 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 (0.38), residues: 524 helix: 1.84 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.42 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.020 0.001 TYR A 527 PHE 0.026 0.002 PHE A 391 TRP 0.035 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4507) covalent geometry : angle 0.56492 / 0.28 ( 6166) SS BOND : bond 0.00359 / 0.24 ( 1) SS BOND : angle 1.10700 / 0.73 ( 2) hydrogen bonds : bond 0.04116 / 2.69 ( 260) hydrogen bonds : angle 4.16431 / 2.85 ( 762) link_NAG-ASN : bond 0.00261 / 0.15 ( 3) link_NAG-ASN : angle 1.56176 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 504 MET cc_start: 0.6822 (mtm) cc_final: 0.6518 (mtm) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.3175 time to fit residues: 15.2535 Evaluate side-chains 44 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.0040 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.158078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.124918 restraints weight = 11136.921| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.24 r_work: 0.3486 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4511 Z= 0.121 Angle : 0.584 8.830 6177 Z= 0.285 Chirality : 0.042 0.197 694 Planarity : 0.004 0.047 725 Dihedral : 9.446 96.795 919 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.12 % Allowed : 14.99 % Favored : 83.89 % 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: 1.24 (0.38), residues: 524 helix: 1.87 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -1.50 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.011 0.001 TYR A 69 PHE 0.030 0.002 PHE A 434 TRP 0.041 0.001 TRP A 166 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4507) covalent geometry : angle 0.58065 / 0.28 ( 6166) SS BOND : bond 0.00359 / 0.24 ( 1) SS BOND : angle 1.14399 / 0.75 ( 2) hydrogen bonds : bond 0.04154 / 2.71 ( 260) hydrogen bonds : angle 4.17714 / 2.86 ( 762) link_NAG-ASN : bond 0.00248 / 0.14 ( 3) link_NAG-ASN : angle 1.59617 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 504 MET cc_start: 0.6859 (mtm) cc_final: 0.6506 (mtm) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.2958 time to fit residues: 15.1562 Evaluate side-chains 47 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121667 restraints weight = 9786.367| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.07 r_work: 0.3452 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4511 Z= 0.146 Angle : 0.626 8.673 6177 Z= 0.308 Chirality : 0.044 0.218 694 Planarity : 0.004 0.050 725 Dihedral : 9.540 96.382 919 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.89 % Allowed : 15.21 % Favored : 83.89 % 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: 1.06 (0.38), residues: 524 helix: 1.74 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.59 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.020 0.001 TYR A 527 PHE 0.030 0.002 PHE A 391 TRP 0.049 0.002 TRP A 166 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 4507) covalent geometry : angle 0.62286 / 0.31 ( 6166) SS BOND : bond 0.00470 / 0.31 ( 1) SS BOND : angle 1.27656 / 0.83 ( 2) hydrogen bonds : bond 0.04838 / 3.14 ( 260) hydrogen bonds : angle 4.34943 / 2.98 ( 762) link_NAG-ASN : bond 0.00223 / 0.13 ( 3) link_NAG-ASN : angle 1.62403 / 0.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.157 Fit side-chains REVERT: A 504 MET cc_start: 0.6956 (mtm) cc_final: 0.6650 (mtm) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.3749 time to fit residues: 19.0321 Evaluate side-chains 48 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119433 restraints weight = 11939.002| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.34 r_work: 0.3411 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4511 Z= 0.168 Angle : 0.670 8.632 6177 Z= 0.331 Chirality : 0.045 0.208 694 Planarity : 0.005 0.052 725 Dihedral : 9.630 96.243 919 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.89 % Allowed : 15.88 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.38), residues: 524 helix: 1.53 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.62 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.015 0.001 TYR A 489 PHE 0.030 0.002 PHE A 391 TRP 0.060 0.002 TRP A 166 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 4507) covalent geometry : angle 0.66729 / 0.33 ( 6166) SS BOND : bond 0.00493 / 0.33 ( 1) SS BOND : angle 1.41828 / 0.91 ( 2) hydrogen bonds : bond 0.05206 / 3.36 ( 260) hydrogen bonds : angle 4.46924 / 3.07 ( 762) link_NAG-ASN : bond 0.00222 / 0.14 ( 3) link_NAG-ASN : angle 1.68306 / 0.88 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.160 Fit side-chains REVERT: A 44 TRP cc_start: 0.7808 (m100) cc_final: 0.7603 (m100) REVERT: A 504 MET cc_start: 0.6960 (mtm) cc_final: 0.6571 (mtm) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.3769 time to fit residues: 19.5603 Evaluate side-chains 49 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.155307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123970 restraints weight = 7136.230| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.59 r_work: 0.3488 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4511 Z= 0.137 Angle : 0.634 8.449 6177 Z= 0.313 Chirality : 0.043 0.206 694 Planarity : 0.004 0.051 725 Dihedral : 9.578 95.357 919 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.67 % Allowed : 16.33 % Favored : 83.00 % 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: 0.95 (0.38), residues: 524 helix: 1.62 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.61 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.010 0.001 TYR A 489 PHE 0.027 0.002 PHE A 391 TRP 0.062 0.002 TRP A 166 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4507) covalent geometry : angle 0.63132 / 0.31 ( 6166) SS BOND : bond 0.00397 / 0.26 ( 1) SS BOND : angle 1.21689 / 0.76 ( 2) hydrogen bonds : bond 0.04594 / 2.99 ( 260) hydrogen bonds : angle 4.36012 / 3.00 ( 762) link_NAG-ASN : bond 0.00262 / 0.16 ( 3) link_NAG-ASN : angle 1.63551 / 0.85 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1443.35 seconds wall clock time: 25 minutes 19.41 seconds (1519.41 seconds total)