Starting phenix.real_space_refine on Thu Jul 2 00:32:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jd9_61385/07_2026/9jd9_61385_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jd9_61385/07_2026/9jd9_61385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jd9_61385/07_2026/9jd9_61385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jd9_61385/07_2026/9jd9_61385.map" model { file = "/net/cci-nas-00/data/ceres_data/9jd9_61385/07_2026/9jd9_61385_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jd9_61385/07_2026/9jd9_61385_neut.cif" } resolution = 3.05 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= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3067 2.51 5 N 670 2.21 5 O 757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 4530 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4373 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 523} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 154 Ad-hoc single atom residues: {' CL': 1, ' NA': 2} Unusual residues: {'C14': 1, 'D10': 2, 'D12': 3, 'DD9': 1, 'HEX': 1, 'HP6': 2, 'NAG': 1, 'OCT': 4, 'TAU': 1} Classifications: {'undetermined': 16, 'water': 2} Link IDs: {None: 16} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.48, per 1000 atoms: 0.33 Number of scatterers: 4530 At special positions: 0 Unit cell: (86.51, 66.465, 88.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 757 8.00 N 670 7.00 C 3067 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 Atom "HETATM 4526 O5 NAG A 719 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A 719 " - " ASN A 190 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 167.6 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 77.2% alpha, 0.4% 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 46 through 59 removed outlier: 3.572A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.803A 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: 6.164A 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 110 through 117 Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.071A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.782A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 removed outlier: 4.366A pdb=" N LYS A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 245 through 266 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.240A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.890A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.637A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.565A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.773A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.561A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 4.168A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (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 450 through 462 removed outlier: 3.733A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.976A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.501A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.076A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.686A pdb=" N THR A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 281 hydrogen bonds defined for protein. 828 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: 0.71 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 883 1.33 - 1.45: 1174 1.45 - 1.57: 2549 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 4653 Sorted by residual: bond pdb=" O2 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.477 1.547 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N THR A 596 " pdb=" CA THR A 596 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.96e+00 bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.75e+00 bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.75e+00 bond pdb=" N GLU A 591 " pdb=" CA GLU A 591 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.44e+00 ... (remaining 4648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 6045 1.40 - 2.80: 189 2.80 - 4.21: 41 4.21 - 5.61: 14 5.61 - 7.01: 2 Bond angle restraints: 6291 Sorted by residual: angle pdb=" CA GLY A 209 " pdb=" C GLY A 209 " pdb=" O GLY A 209 " ideal model delta sigma weight residual 121.60 118.12 3.48 9.70e-01 1.06e+00 1.29e+01 angle pdb=" CA ARG A 583 " pdb=" C ARG A 583 " pdb=" O ARG A 583 " ideal model delta sigma weight residual 122.51 118.01 4.50 1.34e+00 5.57e-01 1.13e+01 angle pdb=" CA ASN A 586 " pdb=" C ASN A 586 " pdb=" O ASN A 586 " ideal model delta sigma weight residual 122.63 118.34 4.29 1.29e+00 6.01e-01 1.11e+01 angle pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" O VAL A 203 " ideal model delta sigma weight residual 120.85 117.35 3.50 1.06e+00 8.90e-01 1.09e+01 angle pdb=" N SER A 205 " pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 111.39 107.13 4.26 1.38e+00 5.25e-01 9.51e+00 ... (remaining 6286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 2343 15.00 - 29.99: 249 29.99 - 44.99: 56 44.99 - 59.99: 15 59.99 - 74.98: 4 Dihedral angle restraints: 2667 sinusoidal: 1079 harmonic: 1588 Sorted by residual: dihedral pdb=" CA PHE A 392 " pdb=" C PHE A 392 " pdb=" N ILE A 393 " pdb=" CA ILE A 393 " ideal model delta harmonic sigma weight residual 180.00 164.08 15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CB MET A 380 " pdb=" CG MET A 380 " pdb=" SD MET A 380 " pdb=" CE MET A 380 " ideal model delta sinusoidal sigma weight residual 180.00 123.23 56.77 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB MET A 327 " pdb=" CG MET A 327 " pdb=" SD MET A 327 " pdb=" CE MET A 327 " ideal model delta sinusoidal sigma weight residual 60.00 112.58 -52.58 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 2664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 595 0.062 - 0.124: 78 0.124 - 0.185: 10 0.185 - 0.247: 0 0.247 - 0.309: 1 Chirality restraints: 684 Sorted by residual: chirality pdb=" C1 NAG A 719 " pdb=" ND2 ASN A 190 " pdb=" C2 NAG A 719 " pdb=" O5 NAG A 719 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA VAL A 590 " pdb=" N VAL A 590 " pdb=" C VAL A 590 " pdb=" CB VAL A 590 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 681 not shown) Planarity restraints: 755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.121 2.00e-02 2.50e+03 1.40e-01 2.44e+02 pdb=" CG ASN A 190 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG A 719 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 719 " -0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG A 719 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 719 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 719 " 0.057 2.00e-02 2.50e+03 pdb=" O7 NAG A 719 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C LEU A 87 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 87 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 88 " 0.012 2.00e-02 2.50e+03 ... (remaining 752 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 64 2.67 - 3.22: 4379 3.22 - 3.78: 7123 3.78 - 4.34: 10196 4.34 - 4.90: 16875 Nonbonded interactions: 38637 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.107 3.040 nonbonded pdb=" OG SER A 301 " pdb="NA NA A 717 " model vdw 2.228 3.210 nonbonded pdb=" O SER A 301 " pdb="NA NA A 717 " model vdw 2.235 3.210 nonbonded pdb=" O2 TAU A 701 " pdb="NA NA A 717 " model vdw 2.245 3.210 nonbonded pdb=" OD2 ASP A 401 " pdb=" O HOH A 801 " model vdw 2.254 3.040 ... (remaining 38632 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.750 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.011 0.683 4656 Z= 1.039 Angle : 0.812 36.743 6296 Z= 0.409 Chirality : 0.045 0.309 684 Planarity : 0.005 0.062 754 Dihedral : 13.108 74.983 1658 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.43 % Allowed : 0.21 % Favored : 99.36 % 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: -0.56 (0.35), residues: 548 helix: 0.28 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.67 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.015 0.001 TYR A 137 PHE 0.020 0.001 PHE A 58 TRP 0.010 0.001 TRP A 113 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.28 ( 4653) covalent geometry : angle 0.61515 / 0.37 ( 6291) SS BOND : bond 0.00141 / 0.09 ( 1) SS BOND : angle 1.58395 / 1.07 ( 2) hydrogen bonds : bond 0.21745 / 14.25 ( 281) hydrogen bonds : angle 7.76372 / 5.49 ( 828) Misc. bond : bond 0.68259 / 45.51 ( 1) link_NAG-ASN : bond 0.04799 / 3.20 ( 1) link_NAG-ASN : angle 24.25370 / 15.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.161 Fit side-chains REVERT: A 179 ASN cc_start: 0.6055 (t0) cc_final: 0.5786 (t0) REVERT: A 202 ASN cc_start: 0.8454 (t0) cc_final: 0.8213 (t0) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.0590 time to fit residues: 5.3559 Evaluate side-chains 58 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.0270 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 212 HIS A 297 GLN A 333 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.118724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.089903 restraints weight = 5570.133| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.04 r_work: 0.2762 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4656 Z= 0.141 Angle : 0.575 8.945 6296 Z= 0.291 Chirality : 0.040 0.144 684 Planarity : 0.005 0.039 754 Dihedral : 7.201 50.230 711 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.71 % Allowed : 4.93 % Favored : 93.36 % 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: 0.26 (0.35), residues: 548 helix: 1.01 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.91 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.025 0.002 TYR A 137 PHE 0.020 0.001 PHE A 58 TRP 0.018 0.001 TRP A 470 HIS 0.006 0.002 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 4653) covalent geometry : angle 0.56463 / 0.29 ( 6291) SS BOND : bond 0.01362 / 0.91 ( 1) SS BOND : angle 3.19226 / 1.69 ( 2) hydrogen bonds : bond 0.04687 / 3.06 ( 281) hydrogen bonds : angle 4.97927 / 3.53 ( 828) Misc. bond : bond 0.00234 / 0.16 ( 1) link_NAG-ASN : bond 0.00277 / 0.18 ( 1) link_NAG-ASN : angle 4.43207 / 2.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.173 Fit side-chains REVERT: A 107 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7957 (mm-30) REVERT: A 172 MET cc_start: 0.7396 (tpt) cc_final: 0.7185 (tpt) REVERT: A 179 ASN cc_start: 0.6224 (t0) cc_final: 0.5944 (t0) REVERT: A 202 ASN cc_start: 0.8453 (t0) cc_final: 0.8156 (t0) REVERT: A 587 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.7200 (ttp-110) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.0558 time to fit residues: 5.0860 Evaluate side-chains 63 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 36 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.118919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.090302 restraints weight = 5582.655| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.02 r_work: 0.2772 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4656 Z= 0.128 Angle : 0.528 9.607 6296 Z= 0.263 Chirality : 0.039 0.144 684 Planarity : 0.004 0.041 754 Dihedral : 6.953 52.859 711 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.57 % Allowed : 7.92 % Favored : 89.51 % 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: 0.67 (0.35), residues: 548 helix: 1.32 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.78 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.026 0.001 TYR A 137 PHE 0.011 0.001 PHE A 474 TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 4653) covalent geometry : angle 0.52125 / 0.26 ( 6291) SS BOND : bond 0.00406 / 0.27 ( 1) SS BOND : angle 1.89632 / 1.02 ( 2) hydrogen bonds : bond 0.04145 / 2.69 ( 281) hydrogen bonds : angle 4.65583 / 3.34 ( 828) Misc. bond : bond 0.00226 / 0.15 ( 1) link_NAG-ASN : bond 0.00108 / 0.07 ( 1) link_NAG-ASN : angle 3.65911 / 1.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8351 (p90) REVERT: A 179 ASN cc_start: 0.6398 (t0) cc_final: 0.6121 (t0) REVERT: A 202 ASN cc_start: 0.8465 (t0) cc_final: 0.8147 (t0) outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 0.0550 time to fit residues: 4.7729 Evaluate side-chains 65 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.0770 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.126790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.099726 restraints weight = 5549.928| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.90 r_work: 0.2834 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4656 Z= 0.119 Angle : 0.513 9.437 6296 Z= 0.255 Chirality : 0.039 0.144 684 Planarity : 0.004 0.041 754 Dihedral : 6.810 57.487 711 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.57 % Allowed : 9.64 % Favored : 87.79 % 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: 0.86 (0.35), residues: 548 helix: 1.45 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.70 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.025 0.001 TYR A 137 PHE 0.010 0.001 PHE A 474 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 4653) covalent geometry : angle 0.50742 / 0.25 ( 6291) SS BOND : bond 0.00411 / 0.27 ( 1) SS BOND : angle 1.38424 / 0.75 ( 2) hydrogen bonds : bond 0.03811 / 2.47 ( 281) hydrogen bonds : angle 4.51136 / 3.24 ( 828) Misc. bond : bond 0.00153 / 0.10 ( 1) link_NAG-ASN : bond 0.00007 / 0.00 ( 1) link_NAG-ASN : angle 3.36471 / 1.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.171 Fit side-chains REVERT: A 69 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8269 (p90) REVERT: A 107 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 179 ASN cc_start: 0.6191 (t0) cc_final: 0.5909 (t0) REVERT: A 202 ASN cc_start: 0.8430 (t0) cc_final: 0.8095 (t0) outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.0608 time to fit residues: 5.1915 Evaluate side-chains 67 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.120525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.091470 restraints weight = 5545.545| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.08 r_work: 0.2773 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4656 Z= 0.124 Angle : 0.513 9.458 6296 Z= 0.254 Chirality : 0.039 0.144 684 Planarity : 0.004 0.042 754 Dihedral : 6.829 55.466 711 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.36 % Allowed : 10.71 % Favored : 86.94 % 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: 0.95 (0.35), residues: 548 helix: 1.54 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.70 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.024 0.001 TYR A 137 PHE 0.010 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 4653) covalent geometry : angle 0.50690 / 0.25 ( 6291) SS BOND : bond 0.00363 / 0.24 ( 1) SS BOND : angle 1.56991 / 0.85 ( 2) hydrogen bonds : bond 0.03761 / 2.43 ( 281) hydrogen bonds : angle 4.46984 / 3.23 ( 828) Misc. bond : bond 0.00127 / 0.08 ( 1) link_NAG-ASN : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : angle 3.34293 / 1.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.163 Fit side-chains REVERT: A 69 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8201 (p90) REVERT: A 107 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 179 ASN cc_start: 0.6379 (t0) cc_final: 0.6092 (t0) REVERT: A 202 ASN cc_start: 0.8547 (t0) cc_final: 0.8233 (t0) REVERT: A 442 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8271 (tp) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.0543 time to fit residues: 4.8744 Evaluate side-chains 67 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.125180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.098302 restraints weight = 5639.479| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.89 r_work: 0.2813 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4656 Z= 0.140 Angle : 0.520 9.452 6296 Z= 0.259 Chirality : 0.039 0.145 684 Planarity : 0.004 0.043 754 Dihedral : 6.901 56.552 711 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.57 % Allowed : 10.92 % Favored : 86.51 % 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: 0.98 (0.35), residues: 548 helix: 1.55 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -1.69 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.025 0.001 TYR A 137 PHE 0.011 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 4653) covalent geometry : angle 0.51465 / 0.26 ( 6291) SS BOND : bond 0.00350 / 0.23 ( 1) SS BOND : angle 1.68698 / 0.92 ( 2) hydrogen bonds : bond 0.03813 / 2.46 ( 281) hydrogen bonds : angle 4.48389 / 3.23 ( 828) Misc. bond : bond 0.00124 / 0.08 ( 1) link_NAG-ASN : bond 0.00042 / 0.03 ( 1) link_NAG-ASN : angle 3.33000 / 1.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.166 Fit side-chains REVERT: A 69 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8035 (p90) REVERT: A 179 ASN cc_start: 0.6386 (t0) cc_final: 0.6099 (t0) REVERT: A 202 ASN cc_start: 0.8548 (t0) cc_final: 0.8205 (t0) REVERT: A 442 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8227 (tp) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.0568 time to fit residues: 5.0638 Evaluate side-chains 66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.119210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.090168 restraints weight = 5566.781| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.05 r_work: 0.2817 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4656 Z= 0.139 Angle : 0.522 9.447 6296 Z= 0.259 Chirality : 0.039 0.144 684 Planarity : 0.004 0.043 754 Dihedral : 6.993 59.066 711 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.78 % Allowed : 11.13 % Favored : 86.08 % 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: 0.99 (0.35), residues: 548 helix: 1.57 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.69 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.025 0.001 TYR A 137 PHE 0.011 0.001 PHE A 50 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4653) covalent geometry : angle 0.51604 / 0.26 ( 6291) SS BOND : bond 0.00350 / 0.23 ( 1) SS BOND : angle 1.65193 / 0.91 ( 2) hydrogen bonds : bond 0.03803 / 2.45 ( 281) hydrogen bonds : angle 4.49601 / 3.24 ( 828) Misc. bond : bond 0.00121 / 0.08 ( 1) link_NAG-ASN : bond 0.00045 / 0.03 ( 1) link_NAG-ASN : angle 3.30524 / 1.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.159 Fit side-chains REVERT: A 179 ASN cc_start: 0.6601 (t0) cc_final: 0.6330 (t0) REVERT: A 202 ASN cc_start: 0.8649 (t0) cc_final: 0.8347 (t0) REVERT: A 442 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8446 (tp) outliers start: 13 outliers final: 11 residues processed: 63 average time/residue: 0.0553 time to fit residues: 4.9235 Evaluate side-chains 67 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.0020 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.119987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.091051 restraints weight = 5642.266| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.05 r_work: 0.2772 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4656 Z= 0.126 Angle : 0.514 9.429 6296 Z= 0.256 Chirality : 0.039 0.144 684 Planarity : 0.004 0.044 754 Dihedral : 7.044 59.804 711 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.36 % Allowed : 11.78 % Favored : 85.87 % 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: 1.05 (0.36), residues: 548 helix: 1.63 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.70 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.024 0.001 TYR A 137 PHE 0.012 0.001 PHE A 50 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4653) covalent geometry : angle 0.50877 / 0.25 ( 6291) SS BOND : bond 0.00360 / 0.24 ( 1) SS BOND : angle 1.49535 / 0.82 ( 2) hydrogen bonds : bond 0.03726 / 2.40 ( 281) hydrogen bonds : angle 4.49111 / 3.23 ( 828) Misc. bond : bond 0.00117 / 0.08 ( 1) link_NAG-ASN : bond 0.00011 / 0.01 ( 1) link_NAG-ASN : angle 3.30998 / 1.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.175 Fit side-chains REVERT: A 69 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7953 (p90) REVERT: A 107 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 179 ASN cc_start: 0.6538 (t0) cc_final: 0.6255 (t0) REVERT: A 202 ASN cc_start: 0.8564 (t0) cc_final: 0.8235 (t0) REVERT: A 442 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8249 (tp) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.0539 time to fit residues: 4.6493 Evaluate side-chains 63 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.120154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.091524 restraints weight = 5536.605| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.02 r_work: 0.2783 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4656 Z= 0.121 Angle : 0.509 9.441 6296 Z= 0.252 Chirality : 0.039 0.144 684 Planarity : 0.004 0.044 754 Dihedral : 6.760 58.643 711 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.14 % Allowed : 12.42 % Favored : 85.44 % 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: 1.12 (0.36), residues: 548 helix: 1.68 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.69 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 263 TYR 0.024 0.001 TYR A 137 PHE 0.012 0.001 PHE A 50 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 4653) covalent geometry : angle 0.50323 / 0.25 ( 6291) SS BOND : bond 0.00333 / 0.22 ( 1) SS BOND : angle 1.45389 / 0.80 ( 2) hydrogen bonds : bond 0.03664 / 2.36 ( 281) hydrogen bonds : angle 4.43580 / 3.20 ( 828) Misc. bond : bond 0.00116 / 0.08 ( 1) link_NAG-ASN : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : angle 3.36147 / 1.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.165 Fit side-chains REVERT: A 107 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7643 (tt0) REVERT: A 179 ASN cc_start: 0.6565 (t0) cc_final: 0.6282 (t0) REVERT: A 202 ASN cc_start: 0.8560 (t0) cc_final: 0.8242 (t0) outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.0540 time to fit residues: 4.5662 Evaluate side-chains 63 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.132692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105948 restraints weight = 5436.712| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.91 r_work: 0.2861 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4656 Z= 0.119 Angle : 0.506 9.468 6296 Z= 0.251 Chirality : 0.039 0.144 684 Planarity : 0.004 0.044 754 Dihedral : 6.576 58.299 711 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 12.63 % Favored : 85.22 % 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: 1.16 (0.36), residues: 548 helix: 1.71 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.69 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.023 0.001 TYR A 137 PHE 0.010 0.001 PHE A 474 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4653) covalent geometry : angle 0.50046 / 0.25 ( 6291) SS BOND : bond 0.00321 / 0.21 ( 1) SS BOND : angle 1.42001 / 0.78 ( 2) hydrogen bonds : bond 0.03626 / 2.34 ( 281) hydrogen bonds : angle 4.41330 / 3.18 ( 828) Misc. bond : bond 0.00115 / 0.08 ( 1) link_NAG-ASN : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : angle 3.34094 / 1.91 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.170 Fit side-chains REVERT: A 107 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7522 (tt0) REVERT: A 179 ASN cc_start: 0.6539 (t0) cc_final: 0.6265 (t0) REVERT: A 202 ASN cc_start: 0.8516 (t0) cc_final: 0.8185 (t0) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.0531 time to fit residues: 4.6687 Evaluate side-chains 63 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.119338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.090692 restraints weight = 5583.454| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.05 r_work: 0.2850 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4656 Z= 0.134 Angle : 0.518 9.446 6296 Z= 0.257 Chirality : 0.039 0.145 684 Planarity : 0.004 0.044 754 Dihedral : 6.666 57.360 711 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 12.63 % Favored : 85.22 % 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: 1.11 (0.36), residues: 548 helix: 1.67 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.69 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.023 0.001 TYR A 137 PHE 0.013 0.001 PHE A 50 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 4653) covalent geometry : angle 0.51191 / 0.26 ( 6291) SS BOND : bond 0.00292 / 0.19 ( 1) SS BOND : angle 1.65195 / 0.90 ( 2) hydrogen bonds : bond 0.03737 / 2.40 ( 281) hydrogen bonds : angle 4.46500 / 3.22 ( 828) Misc. bond : bond 0.00117 / 0.08 ( 1) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 3.36778 / 1.94 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1308.90 seconds wall clock time: 23 minutes 11.16 seconds (1391.16 seconds total)