Starting phenix.real_space_refine on Tue Aug 4 15:00:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2e_38852/08_2026/8y2e_38852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2e_38852/08_2026/8y2e_38852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y2e_38852/08_2026/8y2e_38852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2e_38852/08_2026/8y2e_38852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y2e_38852/08_2026/8y2e_38852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2e_38852/08_2026/8y2e_38852.map" } resolution = 3.03 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= -0.000 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2813 2.51 5 N 659 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 4214 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4163 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 504} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CXQ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.00, per 1000 atoms: 0.24 Number of scatterers: 4214 At special positions: 0 Unit cell: (74.8, 69.7, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 719 8.00 N 659 7.00 C 2813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.04 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 181 " " NAG A 702 " - " ASN A 188 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 142.2 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 79.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.780A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.782A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.598A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.610A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.874A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.830A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.523A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.874A pdb=" N ALA A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 376 Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.685A pdb=" N VAL A 382 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.521A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 467 through 479 removed outlier: 4.111A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.506A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.544A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 4.293A pdb=" N ILE A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 3.593A pdb=" N TYR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.898A pdb=" N TRP A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 268 hydrogen bonds defined for protein. 789 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: 0.53 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1101 1.34 - 1.46: 925 1.46 - 1.58: 2282 1.58 - 1.70: 3 1.70 - 1.82: 34 Bond restraints: 4345 Sorted by residual: bond pdb=" C1 CXQ A 703 " pdb=" C5 CXQ A 703 " ideal model delta sigma weight residual 1.519 1.633 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C1 CXQ A 703 " pdb=" C4 CXQ A 703 " ideal model delta sigma weight residual 1.513 1.594 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C17 CXQ A 703 " pdb=" N1 CXQ A 703 " ideal model delta sigma weight residual 1.448 1.510 -0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" C1 CXQ A 703 " pdb=" O1 CXQ A 703 " ideal model delta sigma weight residual 1.397 1.458 -0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" N ILE A 268 " pdb=" CA ILE A 268 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.49e+00 ... (remaining 4340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5799 1.86 - 3.71: 114 3.71 - 5.57: 15 5.57 - 7.43: 2 7.43 - 9.28: 1 Bond angle restraints: 5931 Sorted by residual: angle pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 112.00 106.62 5.38 1.40e+00 5.10e-01 1.48e+01 angle pdb=" CA ASP A 191 " pdb=" C ASP A 191 " pdb=" O ASP A 191 " ideal model delta sigma weight residual 120.92 117.41 3.51 1.04e+00 9.25e-01 1.14e+01 angle pdb=" CA PHE A 531 " pdb=" CB PHE A 531 " pdb=" CG PHE A 531 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" CA ARG A 606 " pdb=" CB ARG A 606 " pdb=" CG ARG A 606 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA LEU A 250 " pdb=" CB LEU A 250 " pdb=" CG LEU A 250 " ideal model delta sigma weight residual 116.30 125.58 -9.28 3.50e+00 8.16e-02 7.04e+00 ... (remaining 5926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 2330 28.42 - 56.85: 151 56.85 - 85.27: 11 85.27 - 113.70: 0 113.70 - 142.12: 2 Dihedral angle restraints: 2494 sinusoidal: 973 harmonic: 1521 Sorted by residual: dihedral pdb=" C1 CXQ A 703 " pdb=" C6 CXQ A 703 " pdb=" O1 CXQ A 703 " pdb=" C8 CXQ A 703 " ideal model delta sinusoidal sigma weight residual 158.12 16.00 142.12 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C1 CXQ A 703 " pdb=" C6 CXQ A 703 " pdb=" O1 CXQ A 703 " pdb=" C7 CXQ A 703 " ideal model delta sinusoidal sigma weight residual 280.48 139.54 140.94 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CA TRP A 132 " pdb=" C TRP A 132 " pdb=" N LYS A 133 " pdb=" CA LYS A 133 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 529 0.046 - 0.093: 116 0.093 - 0.139: 30 0.139 - 0.185: 2 0.185 - 0.231: 1 Chirality restraints: 678 Sorted by residual: chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2 CXQ A 703 " pdb=" C13 CXQ A 703 " pdb=" C7 CXQ A 703 " pdb=" N1 CXQ A 703 " both_signs ideal model delta sigma weight residual False 2.74 2.92 -0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" C PRO A 584 " pdb=" CB PRO A 584 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 675 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 394 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.54e+00 pdb=" N PRO A 395 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 189 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C CYS A 189 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS A 189 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 190 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.016 2.00e-02 2.50e+03 1.47e-02 2.71e+00 pdb=" CG ASN A 181 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.015 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1154 2.81 - 3.33: 3834 3.33 - 3.85: 6643 3.85 - 4.38: 7416 4.38 - 4.90: 13745 Nonbonded interactions: 32792 Sorted by model distance: nonbonded pdb=" NH1 ARG A 237 " pdb=" OD1 ASN A 466 " model vdw 2.283 3.120 nonbonded pdb=" O ARG A 237 " pdb=" OG1 THR A 241 " model vdw 2.312 3.040 nonbonded pdb=" OG SER A 186 " pdb=" OE2 GLU A 215 " model vdw 2.340 3.040 nonbonded pdb=" N ASP A 79 " pdb=" OD1 ASP A 79 " model vdw 2.409 3.120 nonbonded pdb=" O PHE A 498 " pdb=" NE2 GLN A 611 " model vdw 2.419 3.120 ... (remaining 32787 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.830 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.005 0.114 4348 Z= 0.232 Angle : 0.614 9.283 5939 Z= 0.318 Chirality : 0.041 0.231 678 Planarity : 0.005 0.059 723 Dihedral : 17.534 142.121 1519 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 23.76 % Favored : 76.24 % 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: 1.57 (0.38), residues: 522 helix: 1.92 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.00 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 125 TYR 0.010 0.001 TYR A 575 PHE 0.016 0.001 PHE A 451 TRP 0.013 0.001 TRP A 132 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 ( 4345) covalent geometry : angle 0.60991 / 0.32 ( 5931) SS BOND : bond 0.00707 / 0.37 ( 1) SS BOND : angle 1.67162 / 0.94 ( 2) hydrogen bonds : bond 0.14037 / 8.40 ( 268) hydrogen bonds : angle 4.41491 / 3.30 ( 789) link_NAG-ASN : bond 0.01612 / 0.85 ( 2) link_NAG-ASN : angle 2.17487 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.084 Fit side-chains REVERT: A 126 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 531 PHE cc_start: 0.8123 (t80) cc_final: 0.7252 (t80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0427 time to fit residues: 2.7067 Evaluate side-chains 44 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 30 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.1769 > 50:) overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.131397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.110936 restraints weight = 5100.588| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.77 r_work: 0.3081 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4348 Z= 0.144 Angle : 0.554 7.708 5939 Z= 0.278 Chirality : 0.038 0.129 678 Planarity : 0.005 0.062 723 Dihedral : 9.074 119.151 636 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.17 % Allowed : 22.62 % Favored : 74.21 % 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: 1.78 (0.39), residues: 522 helix: 2.13 (0.28), residues: 361 sheet: None (None), residues: 0 loop : -1.07 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.014 0.001 TYR A 548 PHE 0.014 0.001 PHE A 412 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4345) covalent geometry : angle 0.55208 / 0.28 ( 5931) SS BOND : bond 0.00515 / 0.27 ( 1) SS BOND : angle 1.44421 / 0.81 ( 2) hydrogen bonds : bond 0.05667 / 3.67 ( 268) hydrogen bonds : angle 4.03665 / 3.03 ( 789) link_NAG-ASN : bond 0.00738 / 0.38 ( 2) link_NAG-ASN : angle 1.42358 / 0.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.113 Fit side-chains REVERT: A 126 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 320 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.6009 (t80) REVERT: A 514 GLN cc_start: 0.7081 (tp40) cc_final: 0.6096 (pt0) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 0.0647 time to fit residues: 4.8011 Evaluate side-chains 52 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 517 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.132246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.112098 restraints weight = 5032.134| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.74 r_work: 0.3105 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4348 Z= 0.117 Angle : 0.490 6.313 5939 Z= 0.247 Chirality : 0.037 0.118 678 Planarity : 0.004 0.059 723 Dihedral : 7.867 105.041 636 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.17 % Allowed : 23.08 % Favored : 73.76 % 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: 1.82 (0.39), residues: 522 helix: 2.13 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.18 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.008 0.001 TYR A 575 PHE 0.014 0.001 PHE A 451 TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4345) covalent geometry : angle 0.48876 / 0.25 ( 5931) SS BOND : bond 0.00432 / 0.23 ( 1) SS BOND : angle 1.19367 / 0.68 ( 2) hydrogen bonds : bond 0.04872 / 3.17 ( 268) hydrogen bonds : angle 3.93417 / 2.96 ( 789) link_NAG-ASN : bond 0.00590 / 0.30 ( 2) link_NAG-ASN : angle 1.06866 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.084 Fit side-chains REVERT: A 320 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.5849 (t80) REVERT: A 514 GLN cc_start: 0.6994 (tp40) cc_final: 0.5891 (pt0) outliers start: 14 outliers final: 10 residues processed: 54 average time/residue: 0.0398 time to fit residues: 2.9309 Evaluate side-chains 53 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 14 optimal weight: 0.0170 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.132721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112549 restraints weight = 5025.918| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.74 r_work: 0.3103 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4348 Z= 0.109 Angle : 0.473 5.957 5939 Z= 0.238 Chirality : 0.036 0.114 678 Planarity : 0.004 0.059 723 Dihedral : 7.208 95.057 636 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.30 % Allowed : 21.95 % Favored : 73.76 % 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: 1.84 (0.39), residues: 522 helix: 2.07 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.11 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.008 0.001 TYR A 575 PHE 0.010 0.001 PHE A 98 TRP 0.008 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 4345) covalent geometry : angle 0.47155 / 0.24 ( 5931) SS BOND : bond 0.00371 / 0.20 ( 1) SS BOND : angle 1.05647 / 0.60 ( 2) hydrogen bonds : bond 0.04536 / 2.95 ( 268) hydrogen bonds : angle 3.89769 / 2.93 ( 789) link_NAG-ASN : bond 0.00437 / 0.22 ( 2) link_NAG-ASN : angle 1.02538 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.142 Fit side-chains REVERT: A 126 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7159 (mt-10) REVERT: A 156 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7964 (t80) REVERT: A 320 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.5870 (t80) REVERT: A 514 GLN cc_start: 0.6962 (tp40) cc_final: 0.5776 (pt0) outliers start: 19 outliers final: 12 residues processed: 59 average time/residue: 0.0472 time to fit residues: 3.6839 Evaluate side-chains 56 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.130023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109718 restraints weight = 5126.067| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.75 r_work: 0.3067 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4348 Z= 0.134 Angle : 0.512 6.240 5939 Z= 0.258 Chirality : 0.038 0.116 678 Planarity : 0.005 0.062 723 Dihedral : 7.101 91.559 636 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.75 % Allowed : 21.72 % Favored : 73.53 % 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: 1.70 (0.38), residues: 522 helix: 2.07 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.34 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 606 TYR 0.010 0.001 TYR A 575 PHE 0.016 0.001 PHE A 451 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 4345) covalent geometry : angle 0.51142 / 0.26 ( 5931) SS BOND : bond 0.00420 / 0.22 ( 1) SS BOND : angle 1.18035 / 0.67 ( 2) hydrogen bonds : bond 0.05279 / 3.44 ( 268) hydrogen bonds : angle 4.00098 / 3.01 ( 789) link_NAG-ASN : bond 0.00426 / 0.22 ( 2) link_NAG-ASN : angle 0.96981 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.122 Fit side-chains REVERT: A 156 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 320 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.5876 (t80) REVERT: A 514 GLN cc_start: 0.7007 (tp40) cc_final: 0.5784 (pt0) outliers start: 21 outliers final: 14 residues processed: 59 average time/residue: 0.0529 time to fit residues: 4.2673 Evaluate side-chains 57 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.128639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.108327 restraints weight = 5168.246| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.75 r_work: 0.3049 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4348 Z= 0.138 Angle : 0.517 6.705 5939 Z= 0.262 Chirality : 0.038 0.114 678 Planarity : 0.005 0.062 723 Dihedral : 6.951 87.938 636 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.75 % Allowed : 21.27 % Favored : 73.98 % 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: 1.57 (0.38), residues: 522 helix: 1.98 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.43 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.010 0.001 TYR A 575 PHE 0.016 0.001 PHE A 451 TRP 0.011 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4345) covalent geometry : angle 0.51629 / 0.26 ( 5931) SS BOND : bond 0.00416 / 0.22 ( 1) SS BOND : angle 1.21248 / 0.68 ( 2) hydrogen bonds : bond 0.05423 / 3.54 ( 268) hydrogen bonds : angle 4.03677 / 3.03 ( 789) link_NAG-ASN : bond 0.00387 / 0.20 ( 2) link_NAG-ASN : angle 0.96388 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.095 Fit side-chains REVERT: A 156 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7996 (t80) REVERT: A 320 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.5902 (t80) REVERT: A 514 GLN cc_start: 0.6999 (tp40) cc_final: 0.5743 (pt0) outliers start: 21 outliers final: 16 residues processed: 58 average time/residue: 0.0677 time to fit residues: 5.2455 Evaluate side-chains 60 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.127132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106665 restraints weight = 5245.947| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.78 r_work: 0.3065 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4348 Z= 0.161 Angle : 0.550 6.488 5939 Z= 0.278 Chirality : 0.039 0.122 678 Planarity : 0.005 0.065 723 Dihedral : 6.975 86.816 636 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.98 % Allowed : 21.04 % Favored : 73.98 % 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: 1.39 (0.38), residues: 522 helix: 1.90 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.61 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 606 TYR 0.014 0.001 TYR A 575 PHE 0.016 0.002 PHE A 451 TRP 0.013 0.001 TRP A 132 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 4345) covalent geometry : angle 0.54850 / 0.28 ( 5931) SS BOND : bond 0.00462 / 0.24 ( 1) SS BOND : angle 1.30554 / 0.73 ( 2) hydrogen bonds : bond 0.06003 / 3.92 ( 268) hydrogen bonds : angle 4.12231 / 3.10 ( 789) link_NAG-ASN : bond 0.00369 / 0.19 ( 2) link_NAG-ASN : angle 1.05964 / 0.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.143 Fit side-chains REVERT: A 156 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 320 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.5934 (t80) REVERT: A 514 GLN cc_start: 0.7037 (tp40) cc_final: 0.5776 (pt0) outliers start: 22 outliers final: 18 residues processed: 56 average time/residue: 0.0500 time to fit residues: 3.8633 Evaluate side-chains 59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 31 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.130096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.109845 restraints weight = 5103.313| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.75 r_work: 0.3095 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4348 Z= 0.115 Angle : 0.486 5.932 5939 Z= 0.247 Chirality : 0.037 0.114 678 Planarity : 0.004 0.061 723 Dihedral : 6.717 83.234 636 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.85 % Allowed : 21.95 % Favored : 74.21 % 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: 1.61 (0.38), residues: 522 helix: 2.04 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.52 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 606 TYR 0.009 0.001 TYR A 575 PHE 0.016 0.001 PHE A 451 TRP 0.009 0.001 TRP A 556 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 4345) covalent geometry : angle 0.48481 / 0.25 ( 5931) SS BOND : bond 0.00341 / 0.18 ( 1) SS BOND : angle 1.11299 / 0.63 ( 2) hydrogen bonds : bond 0.04802 / 3.15 ( 268) hydrogen bonds : angle 3.99719 / 3.01 ( 789) link_NAG-ASN : bond 0.00368 / 0.19 ( 2) link_NAG-ASN : angle 0.96400 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.102 Fit side-chains REVERT: A 156 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7936 (t80) REVERT: A 320 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.5975 (t80) REVERT: A 514 GLN cc_start: 0.7030 (tp40) cc_final: 0.5765 (pt0) outliers start: 17 outliers final: 14 residues processed: 53 average time/residue: 0.0597 time to fit residues: 4.1536 Evaluate side-chains 56 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.0170 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.130321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109833 restraints weight = 5204.621| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.79 r_work: 0.3061 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4348 Z= 0.119 Angle : 0.494 5.720 5939 Z= 0.251 Chirality : 0.037 0.112 678 Planarity : 0.004 0.061 723 Dihedral : 6.600 81.267 636 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.85 % Allowed : 22.40 % Favored : 73.76 % 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: 1.65 (0.38), residues: 522 helix: 2.11 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.55 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.010 0.001 TYR A 575 PHE 0.015 0.001 PHE A 451 TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4345) covalent geometry : angle 0.49279 / 0.25 ( 5931) SS BOND : bond 0.00337 / 0.18 ( 1) SS BOND : angle 1.06355 / 0.60 ( 2) hydrogen bonds : bond 0.04888 / 3.20 ( 268) hydrogen bonds : angle 3.99877 / 3.01 ( 789) link_NAG-ASN : bond 0.00355 / 0.18 ( 2) link_NAG-ASN : angle 1.00276 / 0.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.146 Fit side-chains REVERT: A 156 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.7964 (t80) REVERT: A 320 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.5982 (t80) REVERT: A 514 GLN cc_start: 0.7094 (tp40) cc_final: 0.5741 (pt0) outliers start: 17 outliers final: 15 residues processed: 55 average time/residue: 0.0616 time to fit residues: 4.4901 Evaluate side-chains 59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.128432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.108184 restraints weight = 5076.010| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.73 r_work: 0.3046 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4348 Z= 0.138 Angle : 0.525 7.124 5939 Z= 0.267 Chirality : 0.038 0.116 678 Planarity : 0.005 0.062 723 Dihedral : 6.612 80.690 636 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.07 % Allowed : 22.17 % Favored : 73.76 % 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: 1.55 (0.38), residues: 522 helix: 2.03 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.56 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.011 0.001 TYR A 575 PHE 0.017 0.001 PHE A 451 TRP 0.011 0.001 TRP A 132 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4345) covalent geometry : angle 0.52397 / 0.27 ( 5931) SS BOND : bond 0.00402 / 0.21 ( 1) SS BOND : angle 1.16001 / 0.65 ( 2) hydrogen bonds : bond 0.05383 / 3.52 ( 268) hydrogen bonds : angle 4.06179 / 3.06 ( 789) link_NAG-ASN : bond 0.00342 / 0.17 ( 2) link_NAG-ASN : angle 1.07870 / 0.52 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.142 Fit side-chains REVERT: A 156 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8002 (t80) REVERT: A 320 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.5936 (t80) REVERT: A 514 GLN cc_start: 0.7114 (tp40) cc_final: 0.5737 (pt0) outliers start: 18 outliers final: 15 residues processed: 56 average time/residue: 0.0572 time to fit residues: 4.2675 Evaluate side-chains 59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.0050 overall best weight: 0.3102 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.133955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.114169 restraints weight = 5050.884| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.68 r_work: 0.3130 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4348 Z= 0.098 Angle : 0.465 6.455 5939 Z= 0.236 Chirality : 0.036 0.126 678 Planarity : 0.004 0.058 723 Dihedral : 6.342 76.858 636 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.17 % Allowed : 23.08 % Favored : 73.76 % 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: 1.84 (0.38), residues: 522 helix: 2.26 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -1.47 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 606 TYR 0.007 0.001 TYR A 575 PHE 0.017 0.001 PHE A 451 TRP 0.009 0.001 TRP A 556 HIS 0.001 0.000 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 ( 4345) covalent geometry : angle 0.46436 / 0.24 ( 5931) SS BOND : bond 0.00266 / 0.14 ( 1) SS BOND : angle 0.90021 / 0.51 ( 2) hydrogen bonds : bond 0.03965 / 2.60 ( 268) hydrogen bonds : angle 3.90226 / 2.94 ( 789) link_NAG-ASN : bond 0.00375 / 0.19 ( 2) link_NAG-ASN : angle 0.91734 / 0.44 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1033.25 seconds wall clock time: 18 minutes 19.09 seconds (1099.09 seconds total)