Starting phenix.real_space_refine on Wed Jun 4 22:18:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jcz_61378/06_2025/9jcz_61378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jcz_61378/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jcz_61378/06_2025/9jcz_61378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jcz_61378/06_2025/9jcz_61378.map" model { file = "/net/cci-nas-00/data/ceres_data/9jcz_61378/06_2025/9jcz_61378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jcz_61378/06_2025/9jcz_61378.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.27, per 1000 atoms: 1.21 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: 1.27 Conformation dependent library (CDL) restraints added in 955.5 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: 0.46 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: 1.16 Time building geometry restraints manager: 1.49 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: 3.040 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.360 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP A 166 HIS 0.001 0.000 HIS A 161 PHE 0.012 0.001 PHE A 391 TYR 0.012 0.001 TYR A 527 ARG 0.004 0.001 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 3) link_NAG-ASN : angle 0.98462 ( 9) hydrogen bonds : bond 0.14296 ( 260) hydrogen bonds : angle 5.08528 ( 762) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.99631 ( 2) covalent geometry : bond 0.00430 ( 4507) covalent geometry : angle 0.75017 ( 6166) *********************** 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 : 0.458 Fit side-chains REVERT: A 353 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6867 (tm-30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.9162 time to fit residues: 63.6642 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 : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.161023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.128329 restraints weight = 14173.186| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.37 r_work: 0.3540 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1290 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= 0.138 Angle : 0.630 13.531 6177 Z= 0.309 Chirality : 0.042 0.190 694 Planarity : 0.005 0.043 725 Dihedral : 12.042 112.230 919 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.89 % Allowed : 10.74 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.38), residues: 524 helix: 1.61 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.40 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 166 HIS 0.001 0.001 HIS A 212 PHE 0.029 0.002 PHE A 50 TYR 0.015 0.001 TYR A 489 ARG 0.006 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 1.56196 ( 9) hydrogen bonds : bond 0.04854 ( 260) hydrogen bonds : angle 4.38744 ( 762) SS BOND : bond 0.00338 ( 1) SS BOND : angle 1.36065 ( 2) covalent geometry : bond 0.00314 ( 4507) covalent geometry : angle 0.62740 ( 6166) *********************** 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 : 0.450 Fit side-chains REVERT: A 353 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6816 (tm-30) REVERT: A 394 MET cc_start: 0.8506 (ttp) cc_final: 0.8259 (ttp) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.9677 time to fit residues: 51.8372 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 : 0.451 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.161500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130785 restraints weight = 8675.626| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.63 r_work: 0.3592 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1483 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= 0.124 Angle : 0.603 11.659 6177 Z= 0.292 Chirality : 0.042 0.188 694 Planarity : 0.004 0.047 725 Dihedral : 10.152 104.996 919 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.38), residues: 524 helix: 1.58 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.36 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 166 HIS 0.001 0.000 HIS A 161 PHE 0.022 0.002 PHE A 50 TYR 0.010 0.001 TYR A 489 ARG 0.008 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 3) link_NAG-ASN : angle 1.48489 ( 9) hydrogen bonds : bond 0.04306 ( 260) hydrogen bonds : angle 4.25662 ( 762) SS BOND : bond 0.00310 ( 1) SS BOND : angle 1.09949 ( 2) covalent geometry : bond 0.00275 ( 4507) covalent geometry : angle 0.60084 ( 6166) *********************** 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 : 0.468 Fit side-chains REVERT: A 297 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7540 (tp40) REVERT: A 353 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6803 (tm-30) REVERT: A 394 MET cc_start: 0.8530 (ttp) cc_final: 0.8266 (ttp) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.9325 time to fit residues: 48.1835 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 : 0.463 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.160732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.129679 restraints weight = 9586.388| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.75 r_work: 0.3575 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- 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 = 0.36 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1626 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= 0.120 Angle : 0.586 10.795 6177 Z= 0.286 Chirality : 0.042 0.192 694 Planarity : 0.004 0.048 725 Dihedral : 9.885 103.869 919 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.57 % Allowed : 12.98 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.38), residues: 524 helix: 1.58 (0.28), residues: 361 sheet: None (None), residues: 0 loop : -1.29 (0.48), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 PHE 0.027 0.002 PHE A 434 TYR 0.013 0.001 TYR A 527 ARG 0.008 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 3) link_NAG-ASN : angle 1.49998 ( 9) hydrogen bonds : bond 0.04278 ( 260) hydrogen bonds : angle 4.23179 ( 762) SS BOND : bond 0.00340 ( 1) SS BOND : angle 1.18130 ( 2) covalent geometry : bond 0.00266 ( 4507) covalent geometry : angle 0.58324 ( 6166) *********************** 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: 7 poor density : 44 time to evaluate : 0.497 Fit side-chains REVERT: A 353 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6837 (tm-30) outliers start: 7 outliers final: 2 residues processed: 49 average time/residue: 0.8944 time to fit residues: 46.3634 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 : 0.516 ------------------------------------------------------------------------------- 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 50 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.155477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122127 restraints weight = 11908.258| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.34 r_work: 0.3448 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1748 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= 0.136 Angle : 0.605 10.416 6177 Z= 0.298 Chirality : 0.043 0.196 694 Planarity : 0.005 0.050 725 Dihedral : 9.718 102.119 919 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.12 % Allowed : 14.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.38), residues: 524 helix: 1.55 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 166 HIS 0.002 0.001 HIS A 212 PHE 0.029 0.002 PHE A 391 TYR 0.013 0.001 TYR A 489 ARG 0.009 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 3) link_NAG-ASN : angle 1.54908 ( 9) hydrogen bonds : bond 0.04684 ( 260) hydrogen bonds : angle 4.33460 ( 762) SS BOND : bond 0.00431 ( 1) SS BOND : angle 1.24602 ( 2) covalent geometry : bond 0.00309 ( 4507) covalent geometry : angle 0.60256 ( 6166) *********************** 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 52 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.432 Fit side-chains REVERT: A 406 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5918 (mm-30) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.8408 time to fit residues: 44.5265 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 : 0.503 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.156108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121811 restraints weight = 14301.063| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.69 r_work: 0.3439 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1864 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= 0.127 Angle : 0.611 14.455 6177 Z= 0.295 Chirality : 0.042 0.198 694 Planarity : 0.005 0.050 725 Dihedral : 9.615 100.136 919 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.89 % Allowed : 14.99 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.38), residues: 524 helix: 1.68 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.45 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 PHE 0.030 0.002 PHE A 434 TYR 0.012 0.001 TYR A 69 ARG 0.009 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 3) link_NAG-ASN : angle 1.54041 ( 9) hydrogen bonds : bond 0.04390 ( 260) hydrogen bonds : angle 4.26909 ( 762) SS BOND : bond 0.00375 ( 1) SS BOND : angle 1.20942 ( 2) covalent geometry : bond 0.00284 ( 4507) covalent geometry : angle 0.60871 ( 6166) *********************** 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 49 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.445 Fit side-chains REVERT: A 394 MET cc_start: 0.8268 (ttp) cc_final: 0.8057 (ttp) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.9398 time to fit residues: 46.6909 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 : 0.424 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.154109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119992 restraints weight = 13829.889| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.63 r_work: 0.3415 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1924 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= 0.141 Angle : 0.630 14.086 6177 Z= 0.306 Chirality : 0.043 0.201 694 Planarity : 0.005 0.050 725 Dihedral : 9.598 99.203 919 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.67 % Allowed : 14.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.38), residues: 524 helix: 1.66 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -1.59 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 166 HIS 0.001 0.001 HIS A 212 PHE 0.030 0.002 PHE A 391 TYR 0.012 0.001 TYR A 489 ARG 0.009 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 3) link_NAG-ASN : angle 1.56905 ( 9) hydrogen bonds : bond 0.04799 ( 260) hydrogen bonds : angle 4.35653 ( 762) SS BOND : bond 0.00449 ( 1) SS BOND : angle 1.27715 ( 2) covalent geometry : bond 0.00325 ( 4507) covalent geometry : angle 0.62776 ( 6166) *********************** 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: 3 poor density : 46 time to evaluate : 0.447 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.8278 time to fit residues: 42.2668 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 : 0.478 ------------------------------------------------------------------------------- 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 19 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.156342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123570 restraints weight = 9712.165| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.05 r_work: 0.3477 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1971 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= 0.121 Angle : 0.608 13.705 6177 Z= 0.293 Chirality : 0.042 0.200 694 Planarity : 0.005 0.049 725 Dihedral : 9.483 97.333 919 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.38), residues: 524 helix: 1.76 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.50 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 166 HIS 0.001 0.000 HIS A 212 PHE 0.029 0.002 PHE A 434 TYR 0.011 0.001 TYR A 69 ARG 0.009 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 3) link_NAG-ASN : angle 1.56523 ( 9) hydrogen bonds : bond 0.04198 ( 260) hydrogen bonds : angle 4.25298 ( 762) SS BOND : bond 0.00408 ( 1) SS BOND : angle 1.16314 ( 2) covalent geometry : bond 0.00269 ( 4507) covalent geometry : angle 0.60529 ( 6166) *********************** 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 49 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.436 Fit side-chains REVERT: A 324 ARG cc_start: 0.6921 (ttp80) cc_final: 0.6483 (mmm160) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.7822 time to fit residues: 39.1717 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 : 0.371 ------------------------------------------------------------------------------- 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 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.157233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122966 restraints weight = 13588.772| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.63 r_work: 0.3453 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4511 Z= 0.117 Angle : 0.600 13.553 6177 Z= 0.288 Chirality : 0.041 0.198 694 Planarity : 0.004 0.048 725 Dihedral : 9.371 95.559 919 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.89 % Allowed : 15.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.38), residues: 524 helix: 1.82 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -1.47 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 166 HIS 0.002 0.001 HIS A 164 PHE 0.026 0.002 PHE A 391 TYR 0.021 0.001 TYR A 527 ARG 0.009 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 3) link_NAG-ASN : angle 1.58831 ( 9) hydrogen bonds : bond 0.04072 ( 260) hydrogen bonds : angle 4.20863 ( 762) SS BOND : bond 0.00370 ( 1) SS BOND : angle 1.08820 ( 2) covalent geometry : bond 0.00257 ( 4507) covalent geometry : angle 0.59709 ( 6166) *********************** 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 : 0.420 Fit side-chains REVERT: A 324 ARG cc_start: 0.6919 (ttp80) cc_final: 0.6425 (mmm160) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.7820 time to fit residues: 40.0280 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 : 0.494 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.156010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122926 restraints weight = 10215.873| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.14 r_work: 0.3466 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 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 = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4511 Z= 0.128 Angle : 0.628 13.485 6177 Z= 0.302 Chirality : 0.043 0.202 694 Planarity : 0.005 0.049 725 Dihedral : 9.348 94.877 919 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.38), residues: 524 helix: 1.79 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -1.54 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 166 HIS 0.001 0.001 HIS A 164 PHE 0.031 0.002 PHE A 434 TYR 0.011 0.001 TYR A 69 ARG 0.009 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 3) link_NAG-ASN : angle 1.62058 ( 9) hydrogen bonds : bond 0.04354 ( 260) hydrogen bonds : angle 4.26857 ( 762) SS BOND : bond 0.00370 ( 1) SS BOND : angle 1.18417 ( 2) covalent geometry : bond 0.00289 ( 4507) covalent geometry : angle 0.62465 ( 6166) ********************** 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 47 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.501 Fit side-chains REVERT: A 324 ARG cc_start: 0.6970 (ttp80) cc_final: 0.6442 (mmm160) outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.7872 time to fit residues: 38.5991 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 : 0.459 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.0570 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.159931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125442 restraints weight = 14220.805| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.74 r_work: 0.3489 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4511 Z= 0.108 Angle : 0.592 13.385 6177 Z= 0.282 Chirality : 0.041 0.197 694 Planarity : 0.004 0.048 725 Dihedral : 9.130 92.076 919 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.45 % Allowed : 16.11 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.38), residues: 524 helix: 1.91 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -1.45 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 166 HIS 0.002 0.001 HIS A 164 PHE 0.052 0.002 PHE A 391 TYR 0.021 0.001 TYR A 527 ARG 0.009 0.001 ARG A 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 3) link_NAG-ASN : angle 1.66642 ( 9) hydrogen bonds : bond 0.03664 ( 260) hydrogen bonds : angle 4.12514 ( 762) SS BOND : bond 0.00290 ( 1) SS BOND : angle 0.94673 ( 2) covalent geometry : bond 0.00230 ( 4507) covalent geometry : angle 0.58922 ( 6166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3259.44 seconds wall clock time: 56 minutes 26.97 seconds (3386.97 seconds total)