Starting phenix.real_space_refine on Wed Sep 17 04:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jcz_61378/09_2025/9jcz_61378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jcz_61378/09_2025/9jcz_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jcz_61378/09_2025/9jcz_61378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jcz_61378/09_2025/9jcz_61378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jcz_61378/09_2025/9jcz_61378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jcz_61378/09_2025/9jcz_61378.map" } 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-2.0-5805/lib/python3.9/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, 194 Unusual residues: {' CL': 1, ' NA': 2, 'NAG': 3, 'TAU': 1, 'Y01': 4} Classifications: {'undetermined': 11, 'water': 2} Link IDs: {None: 12} 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: 2.19, per 1000 atoms: 0.50 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: 0.33 Conformation dependent library (CDL) restraints added in 328.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.11 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: 0.49 Time building geometry restraints manager: 0.45 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 2.470 nonbonded pdb=" OD1 ASN A 63 " pdb="NA NA A 704 " model vdw 1.931 2.470 nonbonded pdb=" OG ASER A 301 " pdb="NA NA A 704 " model vdw 1.947 2.470 nonbonded pdb=" OD1 ASP A 401 " pdb="NA NA A 703 " model vdw 1.955 2.470 nonbonded pdb=" O GLY A 56 " pdb="NA NA A 703 " model vdw 1.964 2.470 ... (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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.740 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 aren 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 covalent geometry : bond 0.00430 ( 4507) covalent geometry : angle 0.75017 ( 6166) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.99631 ( 2) hydrogen bonds : bond 0.14296 ( 260) hydrogen bonds : angle 5.08528 ( 762) link_NAG-ASN : bond 0.00385 ( 3) link_NAG-ASN : angle 0.98462 ( 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 : 0.172 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: 0.4675 time to fit residues: 32.3265 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 : 0.158 ------------------------------------------------------------------------------- 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: 0.5980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.162196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130420 restraints weight = 10757.114| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.94 r_work: 0.3580 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4511 Z= 0.130 Angle : 0.615 13.243 6177 Z= 0.301 Chirality : 0.042 0.184 694 Planarity : 0.004 0.042 725 Dihedral : 12.078 112.634 919 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.89 % Allowed : 10.07 % Favored : 89.04 % 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: 1.06 (0.38), residues: 524 helix: 1.67 (0.29), residues: 351 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 427 TYR 0.012 0.001 TYR A 527 PHE 0.028 0.002 PHE A 50 TRP 0.020 0.001 TRP A 166 HIS 0.001 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4507) covalent geometry : angle 0.61226 ( 6166) SS BOND : bond 0.00311 ( 1) SS BOND : angle 1.26297 ( 2) hydrogen bonds : bond 0.04647 ( 260) hydrogen bonds : angle 4.32757 ( 762) link_NAG-ASN : bond 0.00292 ( 3) link_NAG-ASN : angle 1.51494 ( 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 51 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.172 Fit side-chains REVERT: A 324 ARG cc_start: 0.5971 (mmm160) cc_final: 0.5693 (mmm160) REVERT: A 353 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6689 (tm-30) REVERT: A 394 MET cc_start: 0.8498 (ttp) cc_final: 0.8252 (ttp) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.4890 time to fit residues: 25.6537 Evaluate side-chains 45 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.159777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127374 restraints weight = 12766.354| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.16 r_work: 0.3534 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1582 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= 0.135 Angle : 0.623 11.562 6177 Z= 0.303 Chirality : 0.043 0.188 694 Planarity : 0.004 0.047 725 Dihedral : 10.326 105.884 919 Min Nonbonded Distance : 2.211 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 aren not related in a simple way. whole: 0.99 (0.38), residues: 524 helix: 1.55 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.35 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.014 0.001 TYR A 489 PHE 0.023 0.002 PHE A 50 TRP 0.022 0.001 TRP A 166 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4507) covalent geometry : angle 0.62076 ( 6166) SS BOND : bond 0.00337 ( 1) SS BOND : angle 1.15969 ( 2) hydrogen bonds : bond 0.04640 ( 260) hydrogen bonds : angle 4.30972 ( 762) link_NAG-ASN : bond 0.00287 ( 3) link_NAG-ASN : angle 1.49645 ( 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 49 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 353 GLN cc_start: 0.7289 (tm-30) cc_final: 0.6845 (tm-30) REVERT: A 394 MET cc_start: 0.8555 (ttp) cc_final: 0.8304 (ttp) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.4276 time to fit residues: 21.6916 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 : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 519 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.161226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129013 restraints weight = 11697.200| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.06 r_work: 0.3559 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4511 Z= 0.116 Angle : 0.576 10.410 6177 Z= 0.280 Chirality : 0.041 0.193 694 Planarity : 0.004 0.047 725 Dihedral : 9.848 103.462 919 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.34 % Allowed : 12.98 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.38), residues: 524 helix: 1.59 (0.28), residues: 361 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.009 0.001 TYR A 69 PHE 0.028 0.002 PHE A 434 TRP 0.025 0.001 TRP A 166 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4507) covalent geometry : angle 0.57337 ( 6166) SS BOND : bond 0.00319 ( 1) SS BOND : angle 1.15599 ( 2) hydrogen bonds : bond 0.04159 ( 260) hydrogen bonds : angle 4.21010 ( 762) link_NAG-ASN : bond 0.00302 ( 3) link_NAG-ASN : angle 1.48053 ( 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 51 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 353 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6839 (tm-30) REVERT: A 394 MET cc_start: 0.8492 (ttp) cc_final: 0.8167 (ttp) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.4370 time to fit residues: 22.5619 Evaluate side-chains 45 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.155307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120505 restraints weight = 15764.369| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.85 r_work: 0.3416 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4511 Z= 0.135 Angle : 0.599 9.623 6177 Z= 0.295 Chirality : 0.042 0.196 694 Planarity : 0.004 0.049 725 Dihedral : 9.663 101.647 919 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.89 % Allowed : 14.77 % 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 aren not related in a simple way. whole: 0.98 (0.38), residues: 524 helix: 1.55 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.41 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.012 0.001 TYR A 489 PHE 0.028 0.002 PHE A 391 TRP 0.029 0.002 TRP A 166 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4507) covalent geometry : angle 0.59569 ( 6166) SS BOND : bond 0.00440 ( 1) SS BOND : angle 1.26525 ( 2) hydrogen bonds : bond 0.04688 ( 260) hydrogen bonds : angle 4.30186 ( 762) link_NAG-ASN : bond 0.00253 ( 3) link_NAG-ASN : angle 1.56622 ( 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 49 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.179 Fit side-chains REVERT: A 324 ARG cc_start: 0.5956 (mmm160) cc_final: 0.5749 (mmm160) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.4370 time to fit residues: 21.6132 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 : 0.143 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 0.0050 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.156921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122961 restraints weight = 12785.119| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.46 r_work: 0.3459 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4511 Z= 0.117 Angle : 0.576 8.984 6177 Z= 0.281 Chirality : 0.042 0.197 694 Planarity : 0.004 0.048 725 Dihedral : 9.561 99.650 919 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.37 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 aren not related in a simple way. whole: 1.10 (0.38), residues: 524 helix: 1.71 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.47 (0.45), residues: 168 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 0.029 0.002 PHE A 434 TRP 0.034 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4507) covalent geometry : angle 0.57270 ( 6166) SS BOND : bond 0.00349 ( 1) SS BOND : angle 1.17197 ( 2) hydrogen bonds : bond 0.04210 ( 260) hydrogen bonds : angle 4.23597 ( 762) link_NAG-ASN : bond 0.00270 ( 3) link_NAG-ASN : angle 1.55626 ( 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 : 0.167 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5955 (mm-30) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.4356 time to fit residues: 20.6995 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 406 GLU 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: 4.9990 chunk 8 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.159519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125510 restraints weight = 11579.028| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.37 r_work: 0.3498 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4511 Z= 0.108 Angle : 0.559 8.550 6177 Z= 0.273 Chirality : 0.041 0.194 694 Planarity : 0.004 0.048 725 Dihedral : 9.375 96.739 919 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.37 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 aren not related in a simple way. whole: 1.26 (0.38), residues: 524 helix: 1.86 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.45 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.012 0.001 TYR A 527 PHE 0.024 0.002 PHE A 391 TRP 0.037 0.001 TRP A 166 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 4507) covalent geometry : angle 0.55613 ( 6166) SS BOND : bond 0.00348 ( 1) SS BOND : angle 0.98716 ( 2) hydrogen bonds : bond 0.03752 ( 260) hydrogen bonds : angle 4.12118 ( 762) link_NAG-ASN : bond 0.00304 ( 3) link_NAG-ASN : angle 1.56494 ( 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 49 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.162 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.4041 time to fit residues: 20.1234 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 : 0.171 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 51 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.158947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124237 restraints weight = 14186.934| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.72 r_work: 0.3475 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4511 Z= 0.113 Angle : 0.578 8.836 6177 Z= 0.279 Chirality : 0.041 0.198 694 Planarity : 0.004 0.047 725 Dihedral : 9.346 95.910 919 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.72 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 aren not related in a simple way. whole: 1.26 (0.38), residues: 524 helix: 1.86 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.47 (0.45), residues: 169 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 0.029 0.002 PHE A 434 TRP 0.043 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4507) covalent geometry : angle 0.57508 ( 6166) SS BOND : bond 0.00326 ( 1) SS BOND : angle 1.02291 ( 2) hydrogen bonds : bond 0.03920 ( 260) hydrogen bonds : angle 4.15526 ( 762) link_NAG-ASN : bond 0.00253 ( 3) link_NAG-ASN : angle 1.60378 ( 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 47 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.133 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.4243 time to fit residues: 20.2172 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 : 0.158 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.156655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122932 restraints weight = 11402.753| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.31 r_work: 0.3463 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2036 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= 0.126 Angle : 0.597 8.548 6177 Z= 0.291 Chirality : 0.042 0.199 694 Planarity : 0.004 0.048 725 Dihedral : 9.357 95.152 919 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.67 % Allowed : 14.77 % Favored : 84.56 % 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: 1.15 (0.38), residues: 524 helix: 1.80 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.58 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.015 0.001 TYR A 104 PHE 0.042 0.002 PHE A 391 TRP 0.048 0.002 TRP A 166 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4507) covalent geometry : angle 0.59362 ( 6166) SS BOND : bond 0.00377 ( 1) SS BOND : angle 1.10151 ( 2) hydrogen bonds : bond 0.04334 ( 260) hydrogen bonds : angle 4.22976 ( 762) link_NAG-ASN : bond 0.00232 ( 3) link_NAG-ASN : angle 1.62518 ( 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 51 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.160 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.3931 time to fit residues: 20.7568 Evaluate side-chains 48 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.156920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122813 restraints weight = 12333.922| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.44 r_work: 0.3458 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2084 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= 0.127 Angle : 0.631 14.795 6177 Z= 0.302 Chirality : 0.043 0.200 694 Planarity : 0.004 0.049 725 Dihedral : 9.316 94.075 919 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.67 % Allowed : 16.11 % 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 aren not related in a simple way. whole: 1.14 (0.38), residues: 524 helix: 1.79 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.58 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.014 0.001 TYR A 104 PHE 0.030 0.002 PHE A 434 TRP 0.054 0.002 TRP A 166 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4507) covalent geometry : angle 0.62786 ( 6166) SS BOND : bond 0.00339 ( 1) SS BOND : angle 1.11554 ( 2) hydrogen bonds : bond 0.04281 ( 260) hydrogen bonds : angle 4.23688 ( 762) link_NAG-ASN : bond 0.00234 ( 3) link_NAG-ASN : angle 1.64209 ( 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 49 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.164 Fit side-chains REVERT: A 324 ARG cc_start: 0.5911 (mmm160) cc_final: 0.5670 (mmm160) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.3882 time to fit residues: 19.7826 Evaluate side-chains 47 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 37 optimal weight: 0.0030 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5648 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.158587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126843 restraints weight = 7101.041| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.62 r_work: 0.3531 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2064 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= 0.114 Angle : 0.606 14.846 6177 Z= 0.288 Chirality : 0.042 0.198 694 Planarity : 0.004 0.047 725 Dihedral : 9.182 92.049 919 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.67 % Allowed : 15.66 % Favored : 83.67 % 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: 1.22 (0.38), residues: 524 helix: 1.84 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.52 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.021 0.001 TYR A 527 PHE 0.046 0.002 PHE A 391 TRP 0.059 0.002 TRP A 166 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4507) covalent geometry : angle 0.60312 ( 6166) SS BOND : bond 0.00295 ( 1) SS BOND : angle 0.96845 ( 2) hydrogen bonds : bond 0.03946 ( 260) hydrogen bonds : angle 4.15626 ( 762) link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 1.65660 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.49 seconds wall clock time: 30 minutes 17.88 seconds (1817.88 seconds total)