Starting phenix.real_space_refine on Tue Aug 4 15:01:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jln_61591/08_2026/9jln_61591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jln_61591/08_2026/9jln_61591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jln_61591/08_2026/9jln_61591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jln_61591/08_2026/9jln_61591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jln_61591/08_2026/9jln_61591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jln_61591/08_2026/9jln_61591.map" } resolution = 2.84 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= 0.079 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 1 4.78 5 C 2898 2.51 5 N 629 2.21 5 O 733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4295 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4139 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 24, 'TRANS': 496} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 156 Unusual residues: {' CL': 1, ' NA': 1, 'NAG': 3, 'TAU': 1, 'Y01': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.09, per 1000 atoms: 0.25 Number of scatterers: 4295 At special positions: 0 Unit cell: (75.492, 71.764, 87.608, 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 1 11.00 O 733 8.00 N 629 7.00 C 2898 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 163 " " NAG A 702 " - " ASN A 179 " " NAG A 703 " - " ASN A 190 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 154.5 milliseconds 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 82.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.756A pdb=" N PHE A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.514A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.765A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (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: 6.097A 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 109 through 117 removed outlier: 4.413A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 153 removed outlier: 4.067A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.933A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.623A pdb=" N ALA A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 266 removed outlier: 4.081A 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: 3.916A 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: 4.316A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.823A pdb=" N ASN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.920A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.836A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 378 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.550A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.194A pdb=" N LEU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 4.200A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.773A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.713A pdb=" N VAL A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.786A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 267 hydrogen bonds defined for protein. 777 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: 0.60 Time building geometry restraints manager: 0.51 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: 646 1.32 - 1.45: 1317 1.45 - 1.57: 2427 1.57 - 1.69: 0 1.69 - 1.82: 47 Bond restraints: 4437 Sorted by residual: bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" CAX Y01 A 706 " pdb=" OAF Y01 A 706 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.42e+00 bond pdb=" CAX Y01 A 708 " pdb=" OAF Y01 A 708 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" CAX Y01 A 707 " pdb=" OAH Y01 A 707 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" CAL Y01 A 706 " pdb=" CAX Y01 A 706 " ideal model delta sigma weight residual 1.540 1.501 0.039 2.00e-02 2.50e+03 3.76e+00 ... (remaining 4432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 5980 2.41 - 4.81: 75 4.81 - 7.21: 9 7.21 - 9.62: 3 9.62 - 12.02: 1 Bond angle restraints: 6068 Sorted by residual: angle pdb=" O1 TAU A 709 " pdb=" S TAU A 709 " pdb=" O2 TAU A 709 " ideal model delta sigma weight residual 113.04 101.02 12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C CYS A 556 " pdb=" N VAL A 557 " pdb=" CA VAL A 557 " ideal model delta sigma weight residual 120.33 122.78 -2.45 8.00e-01 1.56e+00 9.36e+00 angle pdb=" CA LEU A 555 " pdb=" CB LEU A 555 " pdb=" CG LEU A 555 " ideal model delta sigma weight residual 116.30 125.68 -9.38 3.50e+00 8.16e-02 7.19e+00 angle pdb=" CAL Y01 A 708 " pdb=" CAX Y01 A 708 " pdb=" OAH Y01 A 708 " ideal model delta sigma weight residual 115.62 123.15 -7.53 3.00e+00 1.11e-01 6.30e+00 angle pdb=" CAL Y01 A 706 " pdb=" CAX Y01 A 706 " pdb=" OAH Y01 A 706 " ideal model delta sigma weight residual 115.62 123.10 -7.48 3.00e+00 1.11e-01 6.22e+00 ... (remaining 6063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 2535 24.87 - 49.75: 120 49.75 - 74.62: 14 74.62 - 99.50: 9 99.50 - 124.37: 6 Dihedral angle restraints: 2684 sinusoidal: 1184 harmonic: 1500 Sorted by residual: dihedral pdb=" C2 NAG A 703 " pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " pdb=" C5 NAG A 703 " ideal model delta sinusoidal sigma weight residual -62.96 61.41 -124.37 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CAT Y01 A 707 " pdb=" CAR Y01 A 707 " pdb=" CBC Y01 A 707 " pdb=" OAW Y01 A 707 " ideal model delta sinusoidal sigma weight residual 178.96 60.45 118.51 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -119.29 33.29 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 2681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 437 0.032 - 0.065: 169 0.065 - 0.097: 53 0.097 - 0.129: 22 0.129 - 0.161: 3 Chirality restraints: 684 Sorted by residual: chirality pdb=" CBB Y01 A 707 " pdb=" CAC Y01 A 707 " pdb=" CAO Y01 A 707 " pdb=" CBE Y01 A 707 " both_signs ideal model delta sigma weight residual False 2.58 2.41 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 190 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CBE Y01 A 707 " pdb=" CAP Y01 A 707 " pdb=" CBB Y01 A 707 " pdb=" CBI Y01 A 707 " both_signs ideal model delta sigma weight residual False 2.57 2.43 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 681 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C LEU A 87 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 87 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 88 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO A 93 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 478 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C VAL A 478 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A 478 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 479 " 0.008 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 625 2.76 - 3.29: 4243 3.29 - 3.83: 7070 3.83 - 4.36: 7781 4.36 - 4.90: 14146 Nonbonded interactions: 33865 Sorted by model distance: nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.219 3.120 nonbonded pdb=" OG SER A 90 " pdb=" OG1 THR A 512 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.257 3.040 nonbonded pdb=" OAH Y01 A 707 " pdb=" OAH Y01 A 708 " model vdw 2.283 3.040 nonbonded pdb=" NE1 TRP A 65 " pdb=" O PRO A 367 " model vdw 2.303 3.120 ... (remaining 33860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.750 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:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 0.070 4441 Z= 0.190 Angle : 0.657 12.025 6079 Z= 0.320 Chirality : 0.041 0.161 684 Planarity : 0.004 0.039 717 Dihedral : 16.025 124.369 1733 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.39), residues: 519 helix: 1.69 (0.29), residues: 361 sheet: None (None), residues: 0 loop : -1.13 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.017 0.001 TYR A 489 PHE 0.021 0.001 PHE A 338 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 ( 4437) covalent geometry : angle 0.65624 / 0.32 ( 6068) SS BOND : bond 0.00296 / 0.16 ( 1) SS BOND : angle 1.32831 / 0.75 ( 2) hydrogen bonds : bond 0.12643 / 7.93 ( 267) hydrogen bonds : angle 4.66527 / 3.19 ( 777) link_NAG-ASN : bond 0.00220 / 0.11 ( 3) link_NAG-ASN : angle 0.83903 / 0.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3834 time to fit residues: 27.3663 Evaluate side-chains 55 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.175571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.142702 restraints weight = 5343.003| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.36 r_work: 0.3770 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4441 Z= 0.119 Angle : 0.598 11.371 6079 Z= 0.286 Chirality : 0.041 0.185 684 Planarity : 0.004 0.037 717 Dihedral : 13.085 112.336 842 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.57 % Allowed : 8.54 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.39), residues: 519 helix: 1.75 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.38 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 240 TYR 0.011 0.001 TYR A 69 PHE 0.015 0.001 PHE A 338 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 4437) covalent geometry : angle 0.59562 / 0.29 ( 6068) SS BOND : bond 0.00560 / 0.29 ( 1) SS BOND : angle 0.98882 / 0.52 ( 2) hydrogen bonds : bond 0.03950 / 2.49 ( 267) hydrogen bonds : angle 4.13138 / 2.85 ( 777) link_NAG-ASN : bond 0.00245 / 0.12 ( 3) link_NAG-ASN : angle 1.45454 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.091 Fit side-chains REVERT: A 133 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7751 (mm) outliers start: 7 outliers final: 2 residues processed: 65 average time/residue: 0.2976 time to fit residues: 20.4413 Evaluate side-chains 58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 432 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.174205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.141225 restraints weight = 5410.172| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.38 r_work: 0.3748 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4441 Z= 0.121 Angle : 0.611 10.580 6079 Z= 0.289 Chirality : 0.042 0.182 684 Planarity : 0.004 0.040 717 Dihedral : 12.339 111.524 842 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.57 % Allowed : 11.69 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.39), residues: 519 helix: 1.81 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.37 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 240 TYR 0.013 0.001 TYR A 69 PHE 0.015 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4437) covalent geometry : angle 0.60921 / 0.29 ( 6068) SS BOND : bond 0.00371 / 0.20 ( 1) SS BOND : angle 0.94686 / 0.50 ( 2) hydrogen bonds : bond 0.03890 / 2.48 ( 267) hydrogen bonds : angle 4.09864 / 2.83 ( 777) link_NAG-ASN : bond 0.00207 / 0.10 ( 3) link_NAG-ASN : angle 1.39689 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.095 Fit side-chains REVERT: A 69 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.5884 (p90) REVERT: A 133 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7802 (mm) REVERT: A 284 ARG cc_start: 0.8677 (tmt170) cc_final: 0.8350 (tpt90) REVERT: A 380 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7011 (mmp) outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 0.3740 time to fit residues: 25.9536 Evaluate side-chains 57 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 432 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.0060 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.173015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.140076 restraints weight = 5325.937| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.37 r_work: 0.3730 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4441 Z= 0.126 Angle : 0.627 10.515 6079 Z= 0.295 Chirality : 0.042 0.187 684 Planarity : 0.004 0.040 717 Dihedral : 11.273 110.115 842 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.80 % Allowed : 13.03 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.38), residues: 519 helix: 1.78 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.40 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 428 TYR 0.013 0.001 TYR A 532 PHE 0.016 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 4437) covalent geometry : angle 0.62519 / 0.29 ( 6068) SS BOND : bond 0.00303 / 0.16 ( 1) SS BOND : angle 1.11312 / 0.60 ( 2) hydrogen bonds : bond 0.03887 / 2.49 ( 267) hydrogen bonds : angle 4.14379 / 2.87 ( 777) link_NAG-ASN : bond 0.00186 / 0.09 ( 3) link_NAG-ASN : angle 1.41618 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.188 Fit side-chains REVERT: A 69 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.5905 (p90) REVERT: A 133 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7823 (mm) outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 0.3481 time to fit residues: 23.1166 Evaluate side-chains 61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 432 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.173927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.141124 restraints weight = 5330.817| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.35 r_work: 0.3736 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4441 Z= 0.118 Angle : 0.611 10.077 6079 Z= 0.289 Chirality : 0.042 0.187 684 Planarity : 0.004 0.039 717 Dihedral : 10.563 108.978 842 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.02 % Allowed : 14.38 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.38), residues: 519 helix: 1.81 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.37 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 240 TYR 0.014 0.001 TYR A 532 PHE 0.014 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 4437) covalent geometry : angle 0.60852 / 0.29 ( 6068) SS BOND : bond 0.00291 / 0.15 ( 1) SS BOND : angle 1.10046 / 0.60 ( 2) hydrogen bonds : bond 0.03715 / 2.38 ( 267) hydrogen bonds : angle 4.12887 / 2.86 ( 777) link_NAG-ASN : bond 0.00199 / 0.10 ( 3) link_NAG-ASN : angle 1.38408 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.152 Fit side-chains REVERT: A 69 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.5795 (p90) REVERT: A 133 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7814 (mm) REVERT: A 380 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7003 (mmp) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 0.3517 time to fit residues: 26.3141 Evaluate side-chains 62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.173287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140332 restraints weight = 5492.030| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.38 r_work: 0.3733 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4441 Z= 0.118 Angle : 0.633 14.634 6079 Z= 0.296 Chirality : 0.042 0.188 684 Planarity : 0.004 0.040 717 Dihedral : 10.014 107.938 842 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.92 % Allowed : 15.51 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.38), residues: 519 helix: 1.79 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.44 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 240 TYR 0.015 0.001 TYR A 532 PHE 0.015 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4437) covalent geometry : angle 0.63077 / 0.30 ( 6068) SS BOND : bond 0.00305 / 0.16 ( 1) SS BOND : angle 1.11603 / 0.61 ( 2) hydrogen bonds : bond 0.03708 / 2.37 ( 267) hydrogen bonds : angle 4.13746 / 2.87 ( 777) link_NAG-ASN : bond 0.00186 / 0.09 ( 3) link_NAG-ASN : angle 1.40128 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.128 Fit side-chains REVERT: A 69 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.5850 (p90) REVERT: A 133 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7848 (mm) outliers start: 13 outliers final: 5 residues processed: 68 average time/residue: 0.3360 time to fit residues: 24.1261 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.171576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.138748 restraints weight = 5476.762| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.37 r_work: 0.3713 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4441 Z= 0.129 Angle : 0.646 15.247 6079 Z= 0.304 Chirality : 0.043 0.190 684 Planarity : 0.005 0.040 717 Dihedral : 9.877 107.149 842 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.80 % Allowed : 17.30 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.38), residues: 519 helix: 1.73 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.48 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 240 TYR 0.013 0.001 TYR A 69 PHE 0.027 0.002 PHE A 434 TRP 0.011 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4437) covalent geometry : angle 0.64389 / 0.30 ( 6068) SS BOND : bond 0.00351 / 0.18 ( 1) SS BOND : angle 1.15082 / 0.63 ( 2) hydrogen bonds : bond 0.03969 / 2.52 ( 267) hydrogen bonds : angle 4.20015 / 2.92 ( 777) link_NAG-ASN : bond 0.00155 / 0.07 ( 3) link_NAG-ASN : angle 1.43408 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.092 Fit side-chains REVERT: A 69 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.5937 (p90) REVERT: A 133 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7862 (mm) outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.2829 time to fit residues: 21.5045 Evaluate side-chains 61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.171886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139170 restraints weight = 5382.874| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.34 r_work: 0.3717 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4441 Z= 0.128 Angle : 0.656 14.949 6079 Z= 0.310 Chirality : 0.044 0.190 684 Planarity : 0.004 0.040 717 Dihedral : 9.778 106.242 842 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.25 % Allowed : 17.98 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.38), residues: 519 helix: 1.77 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.46 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 240 TYR 0.013 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 4437) covalent geometry : angle 0.65366 / 0.31 ( 6068) SS BOND : bond 0.00327 / 0.17 ( 1) SS BOND : angle 1.20363 / 0.66 ( 2) hydrogen bonds : bond 0.03921 / 2.48 ( 267) hydrogen bonds : angle 4.21781 / 2.93 ( 777) link_NAG-ASN : bond 0.00160 / 0.08 ( 3) link_NAG-ASN : angle 1.43754 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.090 Fit side-chains REVERT: A 69 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.5886 (p90) REVERT: A 133 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7851 (mm) outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 0.3656 time to fit residues: 25.3789 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.172728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.139907 restraints weight = 5485.501| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.38 r_work: 0.3733 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4441 Z= 0.122 Angle : 0.652 15.235 6079 Z= 0.308 Chirality : 0.044 0.192 684 Planarity : 0.004 0.039 717 Dihedral : 9.673 105.388 842 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 19.55 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.38), residues: 519 helix: 1.81 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.45 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 240 TYR 0.013 0.001 TYR A 69 PHE 0.028 0.001 PHE A 434 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 4437) covalent geometry : angle 0.65003 / 0.31 ( 6068) SS BOND : bond 0.00305 / 0.16 ( 1) SS BOND : angle 1.16269 / 0.64 ( 2) hydrogen bonds : bond 0.03820 / 2.43 ( 267) hydrogen bonds : angle 4.21997 / 2.93 ( 777) link_NAG-ASN : bond 0.00171 / 0.08 ( 3) link_NAG-ASN : angle 1.41819 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.086 Fit side-chains REVERT: A 69 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.6707 (p90) REVERT: A 133 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7841 (mm) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.2893 time to fit residues: 19.7446 Evaluate side-chains 60 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 20 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.2399 > 50:) chunk 51 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.173698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.140973 restraints weight = 5440.692| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.37 r_work: 0.3742 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4441 Z= 0.117 Angle : 0.647 15.000 6079 Z= 0.304 Chirality : 0.043 0.193 684 Planarity : 0.004 0.039 717 Dihedral : 9.568 104.336 842 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.57 % Allowed : 20.00 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.38), residues: 519 helix: 1.89 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.51 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 240 TYR 0.014 0.001 TYR A 320 PHE 0.014 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 4437) covalent geometry : angle 0.64455 / 0.30 ( 6068) SS BOND : bond 0.00275 / 0.14 ( 1) SS BOND : angle 1.12585 / 0.62 ( 2) hydrogen bonds : bond 0.03730 / 2.35 ( 267) hydrogen bonds : angle 4.22367 / 2.92 ( 777) link_NAG-ASN : bond 0.00185 / 0.09 ( 3) link_NAG-ASN : angle 1.43320 / 0.79 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.170 Fit side-chains REVERT: A 69 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6753 (p90) REVERT: A 133 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7829 (mm) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.3833 time to fit residues: 25.0473 Evaluate side-chains 61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.173206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.140539 restraints weight = 5358.769| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.34 r_work: 0.3741 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4441 Z= 0.121 Angle : 0.653 15.407 6079 Z= 0.307 Chirality : 0.043 0.190 684 Planarity : 0.004 0.038 717 Dihedral : 9.523 103.659 842 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 20.67 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.38), residues: 519 helix: 1.91 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -1.43 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 240 TYR 0.013 0.001 TYR A 69 PHE 0.028 0.001 PHE A 434 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4437) covalent geometry : angle 0.65050 / 0.31 ( 6068) SS BOND : bond 0.00287 / 0.15 ( 1) SS BOND : angle 1.13638 / 0.63 ( 2) hydrogen bonds : bond 0.03772 / 2.39 ( 267) hydrogen bonds : angle 4.21831 / 2.92 ( 777) link_NAG-ASN : bond 0.00176 / 0.09 ( 3) link_NAG-ASN : angle 1.45165 / 0.80 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.95 seconds wall clock time: 20 minutes 38.58 seconds (1238.58 seconds total)