Starting phenix.real_space_refine on Thu Jul 2 02:40:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgo_60085/07_2026/8zgo_60085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgo_60085/07_2026/8zgo_60085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zgo_60085/07_2026/8zgo_60085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgo_60085/07_2026/8zgo_60085.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgo_60085/07_2026/8zgo_60085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgo_60085/07_2026/8zgo_60085.cif" } resolution = 2.25 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= 0.016 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 Ca 1 9.91 5 Fe 3 7.16 5 S 26 5.16 5 C 3953 2.51 5 N 948 2.21 5 O 1049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s 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: 5980 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5860 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 712} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 118 Ad-hoc single atom residues: {' FE': 1, ' CA': 1} Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2, 'water': 32} Link IDs: {None: 32} Chain breaks: 2 Time building chain proxies: 1.56, per 1000 atoms: 0.26 Number of scatterers: 5980 At special positions: 0 Unit cell: (76.912, 86.108, 101.992, 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) Fe 3 26.01 Ca 1 19.99 S 26 16.00 O 1049 8.00 N 948 7.00 C 3953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 435.8 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 76.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 1 through 3 No H-bonds generated for 'chain 'A' and resid 1 through 3' Processing helix chain 'A' and resid 4 through 33 Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.558A pdb=" N THR A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.642A pdb=" N VAL A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 161 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 182 through 200 Processing helix chain 'A' and resid 226 through 255 removed outlier: 4.961A pdb=" N SER A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE A 253 " --> pdb=" O TRP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 305 removed outlier: 3.534A pdb=" N TYR A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.747A pdb=" N TRP A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 359 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 366 through 394 Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 477 through 490 removed outlier: 3.732A pdb=" N VAL A 488 " --> pdb=" O TRP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 512 Processing helix chain 'A' and resid 516 through 536 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.641A pdb=" N LEU A 540 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 561 removed outlier: 3.531A pdb=" N ALA A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.580A pdb=" N VAL A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 569 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 579 removed outlier: 3.613A pdb=" N HIS A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 607 removed outlier: 3.613A pdb=" N LEU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 617 through 625 removed outlier: 4.454A pdb=" N TYR A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 658 removed outlier: 3.934A pdb=" N ALA A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 686 removed outlier: 3.728A pdb=" N SER A 686 " --> pdb=" O MET A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 702 Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 723 through 746 removed outlier: 4.230A pdb=" N ALA A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.706A pdb=" N VAL A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 398 hydrogen bonds defined for protein. 1164 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: 0.99 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.53: 5563 1.53 - 1.89: 576 1.89 - 2.24: 7 2.24 - 2.60: 0 2.60 - 2.96: 1 Bond restraints: 6147 Sorted by residual: bond pdb=" C PRO A 267 " pdb=" N SER A 269 " ideal model delta sigma weight residual 1.332 2.959 -1.626 1.40e-02 5.10e+03 1.35e+04 bond pdb=" C VAL A 568 " pdb=" N LEU A 569 " ideal model delta sigma weight residual 1.335 1.422 -0.088 1.33e-02 5.65e+03 4.35e+01 bond pdb=" C PRO A 219 " pdb=" O PRO A 219 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.32e-02 5.74e+03 2.52e+01 bond pdb=" C GLY A 65 " pdb=" N GLY A 66 " ideal model delta sigma weight residual 1.326 1.406 -0.079 1.64e-02 3.72e+03 2.34e+01 bond pdb=" C PRO A 364 " pdb=" O PRO A 364 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.14e-02 7.69e+03 2.23e+01 ... (remaining 6142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 7852 2.68 - 5.36: 481 5.36 - 8.05: 61 8.05 - 10.73: 13 10.73 - 13.41: 3 Bond angle restraints: 8410 Sorted by residual: angle pdb=" CA PRO A 267 " pdb=" N PRO A 267 " pdb=" CD PRO A 267 " ideal model delta sigma weight residual 112.00 98.59 13.41 1.40e+00 5.10e-01 9.18e+01 angle pdb=" O GLN A 62 " pdb=" C GLN A 62 " pdb=" N THR A 63 " ideal model delta sigma weight residual 122.12 113.08 9.04 1.06e+00 8.90e-01 7.28e+01 angle pdb=" CA GLN A 62 " pdb=" C GLN A 62 " pdb=" N THR A 63 " ideal model delta sigma weight residual 117.30 126.32 -9.02 1.16e+00 7.43e-01 6.04e+01 angle pdb=" CA GLY A 65 " pdb=" C GLY A 65 " pdb=" O GLY A 65 " ideal model delta sigma weight residual 119.03 110.54 8.49 1.14e+00 7.69e-01 5.55e+01 angle pdb=" C GLU A 218 " pdb=" CA GLU A 218 " pdb=" CB GLU A 218 " ideal model delta sigma weight residual 111.02 122.38 -11.36 1.53e+00 4.27e-01 5.52e+01 ... (remaining 8405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 2999 18.23 - 36.47: 293 36.47 - 54.70: 104 54.70 - 72.94: 11 72.94 - 91.17: 8 Dihedral angle restraints: 3415 sinusoidal: 1287 harmonic: 2128 Sorted by residual: dihedral pdb=" CA PRO A 267 " pdb=" C PRO A 267 " pdb=" N SER A 269 " pdb=" CA SER A 269 " ideal model delta harmonic sigma weight residual 180.00 130.24 49.76 0 5.00e+00 4.00e-02 9.91e+01 dihedral pdb=" C2C HEM A 801 " pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " pdb=" CBC HEM A 801 " ideal model delta sinusoidal sigma weight residual 0.00 -51.48 51.48 2 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" C2B HEM A 802 " pdb=" C3B HEM A 802 " pdb=" CAB HEM A 802 " pdb=" CBB HEM A 802 " ideal model delta sinusoidal sigma weight residual 0.00 44.75 -44.75 2 1.00e+01 1.00e-02 2.38e+01 ... (remaining 3412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 720 0.070 - 0.140: 130 0.140 - 0.210: 33 0.210 - 0.280: 14 0.280 - 0.351: 6 Chirality restraints: 903 Sorted by residual: chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB VAL A 746 " pdb=" CA VAL A 746 " pdb=" CG1 VAL A 746 " pdb=" CG2 VAL A 746 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA THR A 63 " pdb=" N THR A 63 " pdb=" C THR A 63 " pdb=" CB THR A 63 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 900 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 267 " 0.093 2.00e-02 2.50e+03 1.53e-01 2.34e+02 pdb=" C PRO A 267 " -0.260 2.00e-02 2.50e+03 pdb=" O PRO A 267 " 0.125 2.00e-02 2.50e+03 pdb=" N SER A 269 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 266 " 0.123 5.00e-02 4.00e+02 1.72e-01 4.74e+01 pdb=" N PRO A 267 " -0.297 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 594 " 0.024 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" C LEU A 594 " -0.084 2.00e-02 2.50e+03 pdb=" O LEU A 594 " 0.032 2.00e-02 2.50e+03 pdb=" N MET A 595 " 0.028 2.00e-02 2.50e+03 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 321 2.73 - 3.27: 6036 3.27 - 3.81: 10738 3.81 - 4.36: 13168 4.36 - 4.90: 21633 Nonbonded interactions: 51896 Sorted by model distance: nonbonded pdb=" NE2 HIS A 542 " pdb="FE FE A 803 " model vdw 2.182 3.080 nonbonded pdb=" OG SER A 338 " pdb=" OH TYR A 386 " model vdw 2.245 3.040 nonbonded pdb=" ND1 HIS A 490 " pdb="FE FE A 803 " model vdw 2.266 3.080 nonbonded pdb=" O GLY A 161 " pdb=" O ASN A 177 " model vdw 2.288 3.040 nonbonded pdb=" O PHE A 663 " pdb=" NE2 GLN A 741 " model vdw 2.316 3.120 ... (remaining 51891 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: 2.810 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 : 0.023 1.626 6149 Z= 1.601 Angle : 1.320 13.411 8410 Z= 0.899 Chirality : 0.070 0.351 903 Planarity : 0.012 0.172 1033 Dihedral : 16.962 91.173 2059 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.01 % Allowed : 18.23 % Favored : 78.76 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 3.45 % 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: 0.47 (0.32), residues: 736 helix: 0.90 (0.24), residues: 515 sheet: None (None), residues: 0 loop : -0.95 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 724 TYR 0.010 0.001 TYR A 375 PHE 0.018 0.002 PHE A 639 TRP 0.018 0.002 TRP A 342 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.02289 / 1.60 ( 6147) covalent geometry : angle 1.32004 / 0.90 ( 8410) hydrogen bonds : bond 0.16143 / 10.71 ( 398) hydrogen bonds : angle 6.16694 / 4.48 ( 1164) Misc. bond : bond 0.06503 / 3.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.199 Fit side-chains REVERT: A 46 LYS cc_start: 0.7823 (tttt) cc_final: 0.7604 (tmmt) REVERT: A 321 GLU cc_start: 0.7857 (tt0) cc_final: 0.7585 (tm-30) REVERT: A 336 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9179 (mp) REVERT: A 362 LYS cc_start: 0.8000 (mttt) cc_final: 0.7698 (mtmt) REVERT: A 594 LEU cc_start: 0.6632 (tm) cc_final: 0.6413 (tp) REVERT: A 662 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7924 (mm-40) outliers start: 18 outliers final: 8 residues processed: 62 average time/residue: 0.5479 time to fit residues: 35.7551 Evaluate side-chains 56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN A 272 GLN A 511 ASN A 625 GLN A 628 ASN A 676 ASN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.087089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.063546 restraints weight = 8698.056| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.58 r_work: 0.2662 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.254 6149 Z= 0.175 Angle : 0.657 16.086 8410 Z= 0.313 Chirality : 0.043 0.148 903 Planarity : 0.005 0.054 1033 Dihedral : 8.651 83.841 832 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.17 % Allowed : 15.05 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.32), residues: 738 helix: 1.76 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -0.65 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 516 TYR 0.017 0.002 TYR A 328 PHE 0.018 0.002 PHE A 639 TRP 0.019 0.002 TRP A 342 HIS 0.005 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 6147) covalent geometry : angle 0.65691 / 0.31 ( 8410) hydrogen bonds : bond 0.05616 / 3.59 ( 398) hydrogen bonds : angle 4.68808 / 3.34 ( 1164) Misc. bond : bond 0.18542 / 8.89 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.215 Fit side-chains REVERT: A 321 GLU cc_start: 0.8293 (tt0) cc_final: 0.8008 (tm-30) REVERT: A 368 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8028 (ttm170) REVERT: A 498 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7978 (mt-10) REVERT: A 590 LEU cc_start: 0.5975 (pp) cc_final: 0.5641 (pt) outliers start: 13 outliers final: 3 residues processed: 58 average time/residue: 0.6051 time to fit residues: 36.8114 Evaluate side-chains 49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.063442 restraints weight = 8648.421| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 1.58 r_work: 0.2641 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 6149 Z= 0.142 Angle : 0.576 12.261 8410 Z= 0.281 Chirality : 0.041 0.126 903 Planarity : 0.004 0.053 1033 Dihedral : 7.446 86.588 815 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.17 % Allowed : 15.22 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.32), residues: 738 helix: 1.98 (0.24), residues: 517 sheet: -1.28 (1.54), residues: 10 loop : -0.61 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 516 TYR 0.011 0.001 TYR A 328 PHE 0.017 0.001 PHE A 639 TRP 0.020 0.001 TRP A 342 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6147) covalent geometry : angle 0.57616 / 0.28 ( 8410) hydrogen bonds : bond 0.05061 / 3.22 ( 398) hydrogen bonds : angle 4.47944 / 3.21 ( 1164) Misc. bond : bond 0.14328 / 6.87 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.220 Fit side-chains REVERT: A 183 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: A 321 GLU cc_start: 0.8304 (tt0) cc_final: 0.7898 (tm-30) REVERT: A 368 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7919 (ttm170) REVERT: A 498 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7988 (mt-10) outliers start: 13 outliers final: 5 residues processed: 55 average time/residue: 0.5958 time to fit residues: 34.4438 Evaluate side-chains 51 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.066320 restraints weight = 8776.611| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.58 r_work: 0.2696 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.160 6149 Z= 0.108 Angle : 0.534 11.022 8410 Z= 0.257 Chirality : 0.039 0.119 903 Planarity : 0.004 0.051 1033 Dihedral : 7.156 87.122 812 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.84 % Allowed : 16.39 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.02 (0.32), residues: 738 helix: 2.07 (0.24), residues: 523 sheet: -0.88 (1.61), residues: 10 loop : -0.45 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 516 TYR 0.008 0.001 TYR A 328 PHE 0.014 0.001 PHE A 639 TRP 0.019 0.001 TRP A 342 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 6147) covalent geometry : angle 0.53398 / 0.26 ( 8410) hydrogen bonds : bond 0.04233 / 2.69 ( 398) hydrogen bonds : angle 4.32666 / 3.09 ( 1164) Misc. bond : bond 0.11380 / 5.43 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.162 Fit side-chains REVERT: A 183 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: A 498 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7969 (mt-10) outliers start: 11 outliers final: 4 residues processed: 49 average time/residue: 0.5771 time to fit residues: 29.7156 Evaluate side-chains 47 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.089130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.065593 restraints weight = 8910.293| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.60 r_work: 0.2683 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 6149 Z= 0.117 Angle : 0.543 10.935 8410 Z= 0.260 Chirality : 0.039 0.117 903 Planarity : 0.004 0.050 1033 Dihedral : 7.110 89.368 812 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.68 % Allowed : 15.38 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.16 (0.32), residues: 738 helix: 2.20 (0.24), residues: 515 sheet: -0.63 (1.70), residues: 10 loop : -0.38 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 589 TYR 0.010 0.001 TYR A 328 PHE 0.016 0.001 PHE A 639 TRP 0.017 0.001 TRP A 342 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6147) covalent geometry : angle 0.54265 / 0.26 ( 8410) hydrogen bonds : bond 0.04366 / 2.77 ( 398) hydrogen bonds : angle 4.31364 / 3.09 ( 1164) Misc. bond : bond 0.12751 / 6.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.146 Fit side-chains REVERT: A 183 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: A 368 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7957 (ttm170) REVERT: A 498 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 516 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8090 (mmm-85) outliers start: 16 outliers final: 4 residues processed: 51 average time/residue: 0.6000 time to fit residues: 32.1208 Evaluate side-chains 46 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.063389 restraints weight = 8711.997| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 1.58 r_work: 0.2641 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 6149 Z= 0.148 Angle : 0.585 11.869 8410 Z= 0.279 Chirality : 0.041 0.132 903 Planarity : 0.004 0.049 1033 Dihedral : 7.194 88.754 812 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.68 % Allowed : 15.22 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.05 (0.32), residues: 738 helix: 2.11 (0.24), residues: 515 sheet: -0.41 (1.78), residues: 10 loop : -0.42 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 707 TYR 0.013 0.001 TYR A 328 PHE 0.018 0.001 PHE A 639 TRP 0.016 0.001 TRP A 342 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6147) covalent geometry : angle 0.58470 / 0.28 ( 8410) hydrogen bonds : bond 0.05013 / 3.17 ( 398) hydrogen bonds : angle 4.42560 / 3.16 ( 1164) Misc. bond : bond 0.14543 / 6.96 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.216 Fit side-chains REVERT: A 183 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: A 321 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: A 368 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7949 (ttm170) REVERT: A 516 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8081 (mmm-85) outliers start: 16 outliers final: 4 residues processed: 53 average time/residue: 0.6225 time to fit residues: 34.5127 Evaluate side-chains 49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 595 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.064277 restraints weight = 8702.309| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.59 r_work: 0.2659 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 6149 Z= 0.129 Angle : 0.564 11.222 8410 Z= 0.271 Chirality : 0.040 0.122 903 Planarity : 0.004 0.049 1033 Dihedral : 6.815 88.535 810 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.84 % Allowed : 16.56 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.09 (0.32), residues: 738 helix: 2.11 (0.24), residues: 517 sheet: -0.50 (1.73), residues: 10 loop : -0.32 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 655 TYR 0.011 0.001 TYR A 328 PHE 0.018 0.001 PHE A 597 TRP 0.018 0.001 TRP A 342 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6147) covalent geometry : angle 0.56448 / 0.27 ( 8410) hydrogen bonds : bond 0.04669 / 2.96 ( 398) hydrogen bonds : angle 4.36775 / 3.12 ( 1164) Misc. bond : bond 0.12916 / 6.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.218 Fit side-chains REVERT: A 183 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: A 321 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: A 368 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7933 (ttm170) REVERT: A 498 GLU cc_start: 0.8207 (mt-10) cc_final: 0.8007 (mt-10) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.6302 time to fit residues: 32.3454 Evaluate side-chains 49 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.085853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.062133 restraints weight = 8746.565| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.59 r_work: 0.2616 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 6149 Z= 0.171 Angle : 0.607 12.330 8410 Z= 0.292 Chirality : 0.042 0.140 903 Planarity : 0.004 0.049 1033 Dihedral : 6.946 87.375 810 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.17 % Allowed : 16.05 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.92 (0.32), residues: 738 helix: 1.91 (0.23), residues: 526 sheet: -0.50 (1.76), residues: 10 loop : -0.29 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.014 0.001 TYR A 328 PHE 0.023 0.002 PHE A 597 TRP 0.015 0.002 TRP A 342 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 6147) covalent geometry : angle 0.60655 / 0.29 ( 8410) hydrogen bonds : bond 0.05432 / 3.44 ( 398) hydrogen bonds : angle 4.48924 / 3.21 ( 1164) Misc. bond : bond 0.15897 / 7.62 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.165 Fit side-chains REVERT: A 321 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 336 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 368 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8003 (ttm170) outliers start: 13 outliers final: 5 residues processed: 52 average time/residue: 0.6257 time to fit residues: 33.9113 Evaluate side-chains 50 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.063417 restraints weight = 8706.181| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 1.59 r_work: 0.2641 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 6149 Z= 0.138 Angle : 0.583 11.476 8410 Z= 0.280 Chirality : 0.040 0.126 903 Planarity : 0.004 0.050 1033 Dihedral : 6.843 87.601 810 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.84 % Allowed : 16.56 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.01 (0.32), residues: 738 helix: 2.00 (0.24), residues: 523 sheet: -0.56 (1.72), residues: 10 loop : -0.27 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 655 TYR 0.012 0.001 TYR A 328 PHE 0.023 0.001 PHE A 597 TRP 0.019 0.001 TRP A 342 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6147) covalent geometry : angle 0.58255 / 0.28 ( 8410) hydrogen bonds : bond 0.04882 / 3.10 ( 398) hydrogen bonds : angle 4.42921 / 3.17 ( 1164) Misc. bond : bond 0.13638 / 6.53 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.231 Fit side-chains REVERT: A 321 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 368 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7942 (ttm170) REVERT: A 434 MET cc_start: 0.9247 (mmm) cc_final: 0.8877 (mmm) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.6784 time to fit residues: 34.1339 Evaluate side-chains 50 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 24 optimal weight: 3.9990 overall best weight: 0.4906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.088421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.064942 restraints weight = 8722.690| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.59 r_work: 0.2671 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.171 6149 Z= 0.115 Angle : 0.556 10.662 8410 Z= 0.266 Chirality : 0.039 0.119 903 Planarity : 0.004 0.050 1033 Dihedral : 6.725 87.206 810 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.84 % Allowed : 17.39 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.11 (0.32), residues: 738 helix: 2.06 (0.24), residues: 523 sheet: -0.47 (1.74), residues: 10 loop : -0.22 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 517 TYR 0.009 0.001 TYR A 328 PHE 0.023 0.001 PHE A 597 TRP 0.021 0.001 TRP A 342 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 6147) covalent geometry : angle 0.55550 / 0.27 ( 8410) hydrogen bonds : bond 0.04437 / 2.81 ( 398) hydrogen bonds : angle 4.35795 / 3.12 ( 1164) Misc. bond : bond 0.12260 / 5.86 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.183 Fit side-chains REVERT: A 321 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: A 368 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7929 (ttm170) REVERT: A 434 MET cc_start: 0.9245 (mmm) cc_final: 0.8868 (mmm) REVERT: A 590 LEU cc_start: 0.6232 (pp) cc_final: 0.6021 (pt) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.6105 time to fit residues: 26.8126 Evaluate side-chains 45 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 11 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 0.0010 overall best weight: 0.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 HIS ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.067764 restraints weight = 8666.133| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.58 r_work: 0.2727 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 6149 Z= 0.104 Angle : 0.533 10.500 8410 Z= 0.255 Chirality : 0.038 0.120 903 Planarity : 0.004 0.050 1033 Dihedral : 6.517 86.411 810 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.00 % Allowed : 17.39 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.22 (0.33), residues: 738 helix: 2.11 (0.24), residues: 527 sheet: -0.15 (1.91), residues: 10 loop : -0.14 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 517 TYR 0.008 0.001 TYR A 328 PHE 0.018 0.001 PHE A 597 TRP 0.023 0.001 TRP A 342 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 6147) covalent geometry : angle 0.53334 / 0.26 ( 8410) hydrogen bonds : bond 0.03822 / 2.43 ( 398) hydrogen bonds : angle 4.25450 / 3.04 ( 1164) Misc. bond : bond 0.09643 / 4.59 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.19 seconds wall clock time: 40 minutes 33.62 seconds (2433.62 seconds total)