Starting phenix.real_space_refine on Wed Jul 1 23:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jln_61591/07_2026/9jln_61591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jln_61591/07_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_61591/07_2026/9jln_61591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jln_61591/07_2026/9jln_61591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jln_61591/07_2026/9jln_61591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jln_61591/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 154 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'NAG': 3, 'TAU': 1, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.89, per 1000 atoms: 0.21 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: 0.28 Conformation dependent library (CDL) restraints added in 98.0 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: 0.12 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: 0.65 Time building geometry restraints manager: 0.34 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: 0.610 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- 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 : 0.152 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.4025 time to fit residues: 28.7841 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 : 0.145 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.176026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.143024 restraints weight = 5358.116| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.37 r_work: 0.3765 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1040 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= 0.118 Angle : 0.593 11.373 6079 Z= 0.284 Chirality : 0.041 0.182 684 Planarity : 0.004 0.037 717 Dihedral : 13.168 112.743 842 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 8.31 % Favored : 90.11 % 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 (0.39), residues: 519 helix: 1.74 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -1.32 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 240 TYR 0.010 0.001 TYR A 323 PHE 0.014 0.001 PHE A 338 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 4437) covalent geometry : angle 0.59030 / 0.28 ( 6068) SS BOND : bond 0.00154 / 0.08 ( 1) SS BOND : angle 0.77198 / 0.41 ( 2) hydrogen bonds : bond 0.03971 / 2.49 ( 267) hydrogen bonds : angle 4.13379 / 2.85 ( 777) link_NAG-ASN : bond 0.00278 / 0.14 ( 3) link_NAG-ASN : angle 1.43740 / 0.78 ( 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 : 0.156 Fit side-chains REVERT: A 133 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7754 (mm) outliers start: 7 outliers final: 2 residues processed: 65 average time/residue: 0.3691 time to fit residues: 25.3885 Evaluate side-chains 59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.173084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.140032 restraints weight = 5404.234| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.38 r_work: 0.3728 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4441 Z= 0.129 Angle : 0.624 10.755 6079 Z= 0.297 Chirality : 0.042 0.183 684 Planarity : 0.005 0.040 717 Dihedral : 12.442 111.611 842 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.02 % Allowed : 11.01 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.39), residues: 519 helix: 1.72 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.39 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 240 TYR 0.014 0.001 TYR A 69 PHE 0.017 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4437) covalent geometry : angle 0.62175 / 0.30 ( 6068) SS BOND : bond 0.00342 / 0.18 ( 1) SS BOND : angle 0.98924 / 0.53 ( 2) hydrogen bonds : bond 0.04068 / 2.60 ( 267) hydrogen bonds : angle 4.14959 / 2.88 ( 777) link_NAG-ASN : bond 0.00188 / 0.09 ( 3) link_NAG-ASN : angle 1.42078 / 0.77 ( 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: 9 poor density : 62 time to evaluate : 0.164 Fit side-chains REVERT: A 69 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.5934 (p90) REVERT: A 133 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7813 (mm) REVERT: A 380 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6999 (mmp) outliers start: 9 outliers final: 3 residues processed: 65 average time/residue: 0.3875 time to fit residues: 26.4885 Evaluate side-chains 57 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 51 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.174704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141763 restraints weight = 5305.231| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.36 r_work: 0.3749 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1387 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= 0.116 Angle : 0.618 10.725 6079 Z= 0.290 Chirality : 0.041 0.185 684 Planarity : 0.004 0.039 717 Dihedral : 11.294 110.036 842 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 13.71 % Favored : 84.72 % 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: 1.33 (0.38), residues: 519 helix: 1.79 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.34 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 240 TYR 0.013 0.001 TYR A 532 PHE 0.014 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 4437) covalent geometry : angle 0.61549 / 0.29 ( 6068) SS BOND : bond 0.00256 / 0.13 ( 1) SS BOND : angle 1.04685 / 0.57 ( 2) hydrogen bonds : bond 0.03661 / 2.36 ( 267) hydrogen bonds : angle 4.11030 / 2.85 ( 777) link_NAG-ASN : bond 0.00218 / 0.11 ( 3) link_NAG-ASN : angle 1.38801 / 0.76 ( 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 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.149 Fit side-chains REVERT: A 69 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.5782 (p90) REVERT: A 133 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 284 ARG cc_start: 0.8683 (tmt170) cc_final: 0.8394 (tpt90) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 0.4065 time to fit residues: 28.1663 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.173596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140579 restraints weight = 5322.404| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.37 r_work: 0.3727 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1613 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= 0.122 Angle : 0.617 9.996 6079 Z= 0.291 Chirality : 0.042 0.187 684 Planarity : 0.004 0.039 717 Dihedral : 10.671 109.055 842 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.25 % Allowed : 14.83 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.38), residues: 519 helix: 1.76 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.48 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 428 TYR 0.014 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 4437) covalent geometry : angle 0.61449 / 0.29 ( 6068) SS BOND : bond 0.00285 / 0.15 ( 1) SS BOND : angle 1.13111 / 0.62 ( 2) hydrogen bonds : bond 0.03827 / 2.46 ( 267) hydrogen bonds : angle 4.15314 / 2.89 ( 777) link_NAG-ASN : bond 0.00184 / 0.09 ( 3) link_NAG-ASN : angle 1.40819 / 0.77 ( 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 73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.152 Fit side-chains REVERT: A 69 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.5842 (p90) REVERT: A 133 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7839 (mm) REVERT: A 380 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.6997 (mmp) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.3489 time to fit residues: 25.3342 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.172563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139629 restraints weight = 5477.106| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.38 r_work: 0.3717 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4441 Z= 0.129 Angle : 0.643 14.137 6079 Z= 0.302 Chirality : 0.043 0.189 684 Planarity : 0.004 0.039 717 Dihedral : 10.038 107.783 842 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.70 % Allowed : 16.18 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.38), residues: 519 helix: 1.73 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.41 (0.50), 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 0.012 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4437) covalent geometry : angle 0.64091 / 0.30 ( 6068) SS BOND : bond 0.00329 / 0.17 ( 1) SS BOND : angle 1.14228 / 0.63 ( 2) hydrogen bonds : bond 0.03908 / 2.51 ( 267) hydrogen bonds : angle 4.19980 / 2.93 ( 777) link_NAG-ASN : bond 0.00182 / 0.09 ( 3) link_NAG-ASN : angle 1.41484 / 0.78 ( 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 73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.152 Fit side-chains REVERT: A 69 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.5848 (p90) REVERT: A 133 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7856 (mm) REVERT: A 154 GLN cc_start: 0.8475 (mt0) cc_final: 0.8263 (mt0) outliers start: 12 outliers final: 5 residues processed: 70 average time/residue: 0.3972 time to fit residues: 29.2542 Evaluate side-chains 65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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: 0.6980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.170257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.137403 restraints weight = 5456.981| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.37 r_work: 0.3699 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4441 Z= 0.140 Angle : 0.668 15.660 6079 Z= 0.315 Chirality : 0.044 0.191 684 Planarity : 0.005 0.040 717 Dihedral : 9.944 107.298 842 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.80 % Allowed : 17.98 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.38), residues: 519 helix: 1.65 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.47 (0.50), 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 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4437) covalent geometry : angle 0.66569 / 0.31 ( 6068) SS BOND : bond 0.00371 / 0.20 ( 1) SS BOND : angle 1.19976 / 0.66 ( 2) hydrogen bonds : bond 0.04199 / 2.68 ( 267) hydrogen bonds : angle 4.28325 / 2.99 ( 777) link_NAG-ASN : bond 0.00149 / 0.07 ( 3) link_NAG-ASN : angle 1.45082 / 0.80 ( 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 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.158 Fit side-chains REVERT: A 69 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.5960 (p90) REVERT: A 133 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7874 (mm) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.3837 time to fit residues: 27.8867 Evaluate side-chains 62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 28 optimal weight: 0.6980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.173435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.140585 restraints weight = 5365.543| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.36 r_work: 0.3736 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1869 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= 0.117 Angle : 0.643 14.922 6079 Z= 0.303 Chirality : 0.043 0.190 684 Planarity : 0.004 0.039 717 Dihedral : 9.737 106.009 842 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.02 % Allowed : 18.43 % Favored : 79.55 % 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: 1.78 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.39 (0.50), 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 320 PHE 0.025 0.001 PHE A 434 TRP 0.016 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 0.64111 / 0.30 ( 6068) SS BOND : bond 0.00268 / 0.14 ( 1) SS BOND : angle 1.19470 / 0.66 ( 2) hydrogen bonds : bond 0.03725 / 2.37 ( 267) hydrogen bonds : angle 4.20171 / 2.91 ( 777) link_NAG-ASN : bond 0.00193 / 0.10 ( 3) link_NAG-ASN : angle 1.38679 / 0.77 ( 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 72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.111 Fit side-chains REVERT: A 69 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.5678 (p90) REVERT: A 133 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7833 (mm) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 0.3715 time to fit residues: 26.9724 Evaluate side-chains 65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.172642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139809 restraints weight = 5468.046| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.37 r_work: 0.3724 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4441 Z= 0.125 Angle : 0.656 15.240 6079 Z= 0.310 Chirality : 0.043 0.196 684 Planarity : 0.004 0.040 717 Dihedral : 9.678 105.347 842 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.02 % Allowed : 19.10 % 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: 1.30 (0.38), residues: 519 helix: 1.78 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.41 (0.50), 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 0.015 0.001 PHE A 79 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 0.00286 / 0.13 ( 4437) covalent geometry : angle 0.65414 / 0.31 ( 6068) SS BOND : bond 0.00280 / 0.15 ( 1) SS BOND : angle 1.17714 / 0.65 ( 2) hydrogen bonds : bond 0.03893 / 2.47 ( 267) hydrogen bonds : angle 4.22537 / 2.93 ( 777) link_NAG-ASN : bond 0.00155 / 0.08 ( 3) link_NAG-ASN : angle 1.43603 / 0.80 ( 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 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.167 Fit side-chains REVERT: A 69 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.5878 (p90) REVERT: A 133 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7852 (mm) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.3548 time to fit residues: 25.4266 Evaluate side-chains 62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 overall best weight: 0.4814 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.174618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.141790 restraints weight = 5425.728| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.37 r_work: 0.3752 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4441 Z= 0.115 Angle : 0.648 15.457 6079 Z= 0.304 Chirality : 0.043 0.194 684 Planarity : 0.004 0.040 717 Dihedral : 9.556 104.362 842 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.80 % Allowed : 20.45 % 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: 1.35 (0.38), residues: 519 helix: 1.87 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.50 (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 320 PHE 0.028 0.001 PHE A 434 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 4437) covalent geometry : angle 0.64573 / 0.30 ( 6068) SS BOND : bond 0.00511 / 0.27 ( 1) SS BOND : angle 0.78205 / 0.45 ( 2) hydrogen bonds : bond 0.03575 / 2.27 ( 267) hydrogen bonds : angle 4.20223 / 2.91 ( 777) link_NAG-ASN : bond 0.00189 / 0.09 ( 3) link_NAG-ASN : angle 1.55209 / 0.83 ( 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 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.096 Fit side-chains REVERT: A 69 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6704 (p90) REVERT: A 133 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7824 (mm) outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 0.3685 time to fit residues: 25.5739 Evaluate side-chains 65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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: 4.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.0270 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.0770 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS A 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.179091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.146333 restraints weight = 5342.791| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.37 r_work: 0.3811 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4441 Z= 0.107 Angle : 0.627 15.065 6079 Z= 0.294 Chirality : 0.042 0.194 684 Planarity : 0.004 0.041 717 Dihedral : 9.264 102.140 842 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.80 % Allowed : 20.90 % Favored : 77.30 % 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: 1.56 (0.38), residues: 519 helix: 2.00 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.37 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 240 TYR 0.011 0.001 TYR A 69 PHE 0.011 0.001 PHE A 391 TRP 0.016 0.001 TRP A 470 HIS 0.000 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 4437) covalent geometry : angle 0.62564 / 0.29 ( 6068) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.66290 / 0.35 ( 2) hydrogen bonds : bond 0.03241 / 2.03 ( 267) hydrogen bonds : angle 4.10255 / 2.82 ( 777) link_NAG-ASN : bond 0.00255 / 0.13 ( 3) link_NAG-ASN : angle 1.39817 / 0.77 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1321.00 seconds wall clock time: 23 minutes 17.99 seconds (1397.99 seconds total)