Starting phenix.real_space_refine on Fri Sep 11 02:05:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x96_33068/09_2026/7x96_33068_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x96_33068/09_2026/7x96_33068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x96_33068/09_2026/7x96_33068_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x96_33068/09_2026/7x96_33068_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x96_33068/09_2026/7x96_33068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x96_33068/09_2026/7x96_33068.map" } resolution = 3.4 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= 0.002 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: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2159 2.51 5 N 556 2.21 5 O 670 1.98 5 H 3184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6586 Number of models: 1 Model: "" Number of chains: 4 Chain: "G" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3065 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1826 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1624 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.34, per 1000 atoms: 0.20 Number of scatterers: 6586 At special positions: 0 Unit cell: (72.123, 86.216, 92.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 670 8.00 N 556 7.00 C 2159 6.00 H 3184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " BETA1-6 " NAG A 1 " - " FUC A 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 277.2 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 14.3% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 364 through 371 removed outlier: 4.481A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 389 Processing helix chain 'G' and resid 403 through 408 removed outlier: 3.922A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.524A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.581A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.720A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 379 through 380 Processing sheet with id=AA5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.518A pdb=" N VAL H 116 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA9, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.677A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 264 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: 1.19 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3183 1.03 - 1.23: 20 1.23 - 1.43: 1514 1.43 - 1.62: 1934 1.62 - 1.82: 21 Bond restraints: 6672 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 MAN A 5 " pdb=" C2 MAN A 5 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 6667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11726 1.51 - 3.03: 178 3.03 - 4.54: 26 4.54 - 6.06: 7 6.06 - 7.57: 4 Bond angle restraints: 11941 Sorted by residual: angle pdb=" CA ARG L 97 " pdb=" CB ARG L 97 " pdb=" CG ARG L 97 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N VAL H 102 " pdb=" CA VAL H 102 " pdb=" C VAL H 102 " ideal model delta sigma weight residual 110.21 106.93 3.28 1.13e+00 7.83e-01 8.43e+00 angle pdb=" C PRO L 96 " pdb=" N ARG L 97 " pdb=" CA ARG L 97 " ideal model delta sigma weight residual 122.30 125.62 -3.32 1.35e+00 5.49e-01 6.04e+00 angle pdb=" CB ARG L 97 " pdb=" CG ARG L 97 " pdb=" CD ARG L 97 " ideal model delta sigma weight residual 111.30 116.67 -5.37 2.30e+00 1.89e-01 5.45e+00 angle pdb=" C3 MAN A 4 " pdb=" C2 MAN A 4 " pdb=" O2 MAN A 4 " ideal model delta sigma weight residual 111.77 105.58 6.19 3.00e+00 1.11e-01 4.25e+00 ... (remaining 11936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 3063 21.62 - 43.23: 166 43.23 - 64.85: 57 64.85 - 86.47: 13 86.47 - 108.08: 5 Dihedral angle restraints: 3304 sinusoidal: 1796 harmonic: 1508 Sorted by residual: dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual 93.00 -178.36 -88.64 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 146.29 -53.29 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 454 0.054 - 0.107: 55 0.107 - 0.161: 25 0.161 - 0.214: 0 0.214 - 0.268: 1 Chirality restraints: 535 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2 BMA A 3 " pdb=" C1 BMA A 3 " pdb=" C3 BMA A 3 " pdb=" O2 BMA A 3 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE G 402 " pdb=" N ILE G 402 " pdb=" C ILE G 402 " pdb=" CB ILE G 402 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 532 not shown) Planarity restraints: 1007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 97 " 0.199 9.50e-02 1.11e+02 6.65e-02 4.79e+00 pdb=" NE ARG L 97 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG L 97 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG L 97 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG L 97 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG L 97 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO G 521 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO L 96 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.015 5.00e-02 4.00e+02 ... (remaining 1004 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 288 2.17 - 2.78: 12644 2.78 - 3.38: 17363 3.38 - 3.99: 23147 3.99 - 4.60: 35239 Nonbonded interactions: 88681 Sorted by model distance: nonbonded pdb=" O TRP G 353 " pdb="HH12 ARG G 466 " model vdw 1.562 2.450 nonbonded pdb=" HG SER L 12 " pdb=" O ASP L 107 " model vdw 1.624 2.450 nonbonded pdb=" H LEU G 455 " pdb=" O PRO G 491 " model vdw 1.641 2.450 nonbonded pdb=" OE1 GLU L 81 " pdb=" H GLU L 81 " model vdw 1.643 2.450 nonbonded pdb=" OE1 GLU H 89 " pdb=" H GLU H 89 " model vdw 1.649 2.450 ... (remaining 88676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.370 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: 0.030 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.003 0.033 3500 Z= 0.158 Angle : 0.615 7.571 4777 Z= 0.301 Chirality : 0.045 0.268 535 Planarity : 0.005 0.086 603 Dihedral : 15.740 108.084 1322 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.42), residues: 421 helix: -1.99 (1.15), residues: 19 sheet: -0.82 (0.42), residues: 167 loop : -0.77 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 97 TYR 0.011 0.001 TYR H 80 PHE 0.005 0.001 PHE G 400 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 3488) covalent geometry : angle 0.60890 / 0.30 ( 4747) SS BOND : bond 0.00201 / 0.10 ( 6) SS BOND : angle 0.82262 / 0.46 ( 12) hydrogen bonds : bond 0.19473 / 13.18 ( 99) hydrogen bonds : angle 7.60033 / 5.42 ( 264) link_ALPHA1-3 : bond 0.00427 / 0.22 ( 1) link_ALPHA1-3 : angle 1.55077 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00442 / 0.23 ( 1) link_ALPHA1-6 : angle 1.51718 / 0.76 ( 3) link_BETA1-4 : bond 0.00288 / 0.14 ( 2) link_BETA1-4 : angle 1.16527 / 0.58 ( 6) link_BETA1-6 : bond 0.00415 / 0.22 ( 1) link_BETA1-6 : angle 1.55489 / 0.76 ( 3) link_NAG-ASN : bond 0.00102 / 0.05 ( 1) link_NAG-ASN : angle 1.75245 / 1.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 493 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8640 (tp-100) REVERT: H 62 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8353 (tm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1513 time to fit residues: 13.0734 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** 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 = 0.2964 r_free = 0.2964 target = 0.057061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.046746 restraints weight = 35353.520| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 4.26 r_work: 0.2566 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 3500 Z= 0.356 Angle : 0.643 6.700 4777 Z= 0.337 Chirality : 0.043 0.209 535 Planarity : 0.005 0.039 603 Dihedral : 10.001 71.261 582 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.37 % Allowed : 8.74 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.80 (0.40), residues: 421 helix: -2.45 (1.00), residues: 20 sheet: -1.04 (0.42), residues: 155 loop : -1.15 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 97 TYR 0.014 0.002 TYR L 49 PHE 0.011 0.001 PHE H 64 TRP 0.006 0.001 TRP G 353 HIS 0.005 0.002 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.36 ( 3488) covalent geometry : angle 0.62297 / 0.33 ( 4747) SS BOND : bond 0.00276 / 0.17 ( 6) SS BOND : angle 0.99289 / 0.55 ( 12) hydrogen bonds : bond 0.03986 / 2.65 ( 99) hydrogen bonds : angle 6.10211 / 4.22 ( 264) link_ALPHA1-3 : bond 0.00410 / 0.22 ( 1) link_ALPHA1-3 : angle 4.42213 / 2.31 ( 3) link_ALPHA1-6 : bond 0.00696 / 0.37 ( 1) link_ALPHA1-6 : angle 2.03359 / 0.99 ( 3) link_BETA1-4 : bond 0.00560 / 0.29 ( 2) link_BETA1-4 : angle 1.89074 / 1.00 ( 6) link_BETA1-6 : bond 0.00354 / 0.19 ( 1) link_BETA1-6 : angle 1.78661 / 0.74 ( 3) link_NAG-ASN : bond 0.00261 / 0.14 ( 1) link_NAG-ASN : angle 2.65426 / 1.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8591 (tp-100) REVERT: H 62 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8677 (tm-30) REVERT: H 82 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7964 (tm-30) REVERT: L 38 GLN cc_start: 0.8800 (tp40) cc_final: 0.8532 (tp40) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.1517 time to fit residues: 11.1592 Evaluate side-chains 62 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.058866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.048451 restraints weight = 33853.756| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 4.26 r_work: 0.2606 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3500 Z= 0.123 Angle : 0.541 5.026 4777 Z= 0.279 Chirality : 0.043 0.153 535 Planarity : 0.004 0.029 603 Dihedral : 6.882 48.430 582 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.37 % Allowed : 9.56 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.52 (0.41), residues: 421 helix: -2.13 (1.08), residues: 20 sheet: -0.71 (0.43), residues: 151 loop : -1.08 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 454 TYR 0.006 0.001 TYR G 380 PHE 0.008 0.001 PHE H 64 TRP 0.004 0.001 TRP G 436 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3488) covalent geometry : angle 0.53004 / 0.28 ( 4747) SS BOND : bond 0.00167 / 0.08 ( 6) SS BOND : angle 0.81044 / 0.39 ( 12) hydrogen bonds : bond 0.03299 / 2.25 ( 99) hydrogen bonds : angle 5.88791 / 4.12 ( 264) link_ALPHA1-3 : bond 0.01003 / 0.53 ( 1) link_ALPHA1-3 : angle 2.63865 / 1.41 ( 3) link_ALPHA1-6 : bond 0.00707 / 0.37 ( 1) link_ALPHA1-6 : angle 1.63170 / 0.81 ( 3) link_BETA1-4 : bond 0.00427 / 0.20 ( 2) link_BETA1-4 : angle 1.39501 / 0.72 ( 6) link_BETA1-6 : bond 0.00181 / 0.10 ( 1) link_BETA1-6 : angle 1.21189 / 0.60 ( 3) link_NAG-ASN : bond 0.00113 / 0.06 ( 1) link_NAG-ASN : angle 2.03284 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8505 (tp-100) REVERT: H 62 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8654 (tm-30) REVERT: H 82 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7862 (tm-30) REVERT: L 38 GLN cc_start: 0.8705 (tp40) cc_final: 0.8434 (tp40) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.1214 time to fit residues: 9.7788 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 409 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 = 0.3032 r_free = 0.3032 target = 0.059480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.049517 restraints weight = 34112.681| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.18 r_work: 0.2633 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3500 Z= 0.120 Angle : 0.524 5.144 4777 Z= 0.268 Chirality : 0.042 0.156 535 Planarity : 0.004 0.028 603 Dihedral : 5.997 46.891 582 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.37 % Allowed : 10.11 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.41), residues: 421 helix: -2.06 (1.09), residues: 20 sheet: -0.61 (0.44), residues: 152 loop : -1.00 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 105 TYR 0.026 0.001 TYR L 49 PHE 0.007 0.001 PHE H 64 TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 3488) covalent geometry : angle 0.51249 / 0.27 ( 4747) SS BOND : bond 0.00157 / 0.08 ( 6) SS BOND : angle 0.75632 / 0.36 ( 12) hydrogen bonds : bond 0.02854 / 1.90 ( 99) hydrogen bonds : angle 5.70578 / 3.98 ( 264) link_ALPHA1-3 : bond 0.01188 / 0.63 ( 1) link_ALPHA1-3 : angle 2.27971 / 1.22 ( 3) link_ALPHA1-6 : bond 0.00267 / 0.14 ( 1) link_ALPHA1-6 : angle 1.67795 / 0.88 ( 3) link_BETA1-4 : bond 0.00351 / 0.17 ( 2) link_BETA1-4 : angle 1.53431 / 0.77 ( 6) link_BETA1-6 : bond 0.00267 / 0.14 ( 1) link_BETA1-6 : angle 1.28843 / 0.62 ( 3) link_NAG-ASN : bond 0.00241 / 0.13 ( 1) link_NAG-ASN : angle 2.16865 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8580 (tp-100) REVERT: G 427 ASP cc_start: 0.8815 (m-30) cc_final: 0.8512 (p0) REVERT: H 62 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8614 (tm-30) REVERT: H 82 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7931 (tm-30) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.1383 time to fit residues: 10.9376 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 9 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.5784 > 50:) chunk 40 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 409 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 = 0.3038 r_free = 0.3038 target = 0.059693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.049577 restraints weight = 34083.050| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.23 r_work: 0.2638 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3500 Z= 0.115 Angle : 0.513 5.115 4777 Z= 0.262 Chirality : 0.042 0.135 535 Planarity : 0.003 0.028 603 Dihedral : 5.744 46.763 582 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.64 % Allowed : 10.93 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.26 (0.42), residues: 421 helix: -1.92 (1.12), residues: 20 sheet: -0.50 (0.44), residues: 152 loop : -0.92 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 55 TYR 0.024 0.001 TYR L 49 PHE 0.007 0.001 PHE H 64 TRP 0.005 0.001 TRP G 436 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 3488) covalent geometry : angle 0.50183 / 0.26 ( 4747) SS BOND : bond 0.00150 / 0.07 ( 6) SS BOND : angle 0.75216 / 0.36 ( 12) hydrogen bonds : bond 0.02726 / 1.81 ( 99) hydrogen bonds : angle 5.57237 / 3.89 ( 264) link_ALPHA1-3 : bond 0.01041 / 0.55 ( 1) link_ALPHA1-3 : angle 2.36729 / 1.27 ( 3) link_ALPHA1-6 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-6 : angle 1.56956 / 0.83 ( 3) link_BETA1-4 : bond 0.00303 / 0.14 ( 2) link_BETA1-4 : angle 1.49846 / 0.76 ( 6) link_BETA1-6 : bond 0.00216 / 0.11 ( 1) link_BETA1-6 : angle 1.24103 / 0.60 ( 3) link_NAG-ASN : bond 0.00171 / 0.09 ( 1) link_NAG-ASN : angle 2.21751 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8576 (tp-100) REVERT: G 427 ASP cc_start: 0.8803 (m-30) cc_final: 0.8508 (p0) REVERT: H 62 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8625 (tm-30) REVERT: H 82 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7997 (tm-30) outliers start: 6 outliers final: 6 residues processed: 63 average time/residue: 0.1360 time to fit residues: 10.7375 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 409 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 = 0.3014 r_free = 0.3014 target = 0.060001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.049112 restraints weight = 34413.408| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 4.27 r_work: 0.2597 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3500 Z= 0.223 Angle : 0.548 4.605 4777 Z= 0.284 Chirality : 0.042 0.134 535 Planarity : 0.004 0.028 603 Dihedral : 5.648 46.833 582 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 1.64 % Allowed : 11.48 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.41), residues: 421 helix: -2.01 (1.10), residues: 20 sheet: -0.71 (0.42), residues: 156 loop : -0.96 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 55 TYR 0.024 0.001 TYR L 49 PHE 0.008 0.001 PHE H 64 TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 3488) covalent geometry : angle 0.53541 / 0.28 ( 4747) SS BOND : bond 0.00156 / 0.07 ( 6) SS BOND : angle 0.79048 / 0.40 ( 12) hydrogen bonds : bond 0.03099 / 2.03 ( 99) hydrogen bonds : angle 5.48030 / 3.83 ( 264) link_ALPHA1-3 : bond 0.00772 / 0.41 ( 1) link_ALPHA1-3 : angle 2.60556 / 1.40 ( 3) link_ALPHA1-6 : bond 0.00308 / 0.16 ( 1) link_ALPHA1-6 : angle 1.58113 / 0.84 ( 3) link_BETA1-4 : bond 0.00332 / 0.17 ( 2) link_BETA1-4 : angle 1.53773 / 0.75 ( 6) link_BETA1-6 : bond 0.00341 / 0.18 ( 1) link_BETA1-6 : angle 1.52265 / 0.72 ( 3) link_NAG-ASN : bond 0.00093 / 0.05 ( 1) link_NAG-ASN : angle 2.51329 / 1.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9348 (tt0) cc_final: 0.9030 (tm-30) REVERT: G 414 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8619 (tp40) REVERT: G 427 ASP cc_start: 0.8798 (m-30) cc_final: 0.8535 (p0) REVERT: H 62 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8676 (tm-30) REVERT: H 80 TYR cc_start: 0.8734 (m-80) cc_final: 0.8512 (m-80) REVERT: L 82 ASP cc_start: 0.7824 (m-30) cc_final: 0.7620 (m-30) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.1188 time to fit residues: 9.0274 Evaluate side-chains 61 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 409 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 = 0.3022 r_free = 0.3022 target = 0.060273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.049392 restraints weight = 33542.176| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 4.29 r_work: 0.2612 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3500 Z= 0.138 Angle : 0.529 5.071 4777 Z= 0.274 Chirality : 0.042 0.137 535 Planarity : 0.004 0.031 603 Dihedral : 5.535 47.196 582 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.64 % Allowed : 12.84 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.36 (0.41), residues: 421 helix: -1.86 (1.11), residues: 20 sheet: -0.56 (0.43), residues: 153 loop : -1.01 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 55 TYR 0.019 0.001 TYR L 49 PHE 0.009 0.001 PHE G 464 TRP 0.006 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 3488) covalent geometry : angle 0.51720 / 0.27 ( 4747) SS BOND : bond 0.00153 / 0.07 ( 6) SS BOND : angle 0.79615 / 0.38 ( 12) hydrogen bonds : bond 0.02873 / 1.93 ( 99) hydrogen bonds : angle 5.48530 / 3.87 ( 264) link_ALPHA1-3 : bond 0.00927 / 0.49 ( 1) link_ALPHA1-3 : angle 2.35492 / 1.27 ( 3) link_ALPHA1-6 : bond 0.00380 / 0.20 ( 1) link_ALPHA1-6 : angle 1.51989 / 0.81 ( 3) link_BETA1-4 : bond 0.00277 / 0.14 ( 2) link_BETA1-4 : angle 1.49496 / 0.76 ( 6) link_BETA1-6 : bond 0.00214 / 0.11 ( 1) link_BETA1-6 : angle 1.30315 / 0.63 ( 3) link_NAG-ASN : bond 0.00095 / 0.05 ( 1) link_NAG-ASN : angle 2.26368 / 1.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9350 (tt0) cc_final: 0.9021 (tm-30) REVERT: G 414 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8718 (tp40) REVERT: G 427 ASP cc_start: 0.8793 (m-30) cc_final: 0.8526 (p0) REVERT: H 62 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8629 (tm-30) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.1245 time to fit residues: 9.4515 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3022 r_free = 0.3022 target = 0.060303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.049470 restraints weight = 34096.896| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 4.26 r_work: 0.2608 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3500 Z= 0.138 Angle : 0.524 5.069 4777 Z= 0.272 Chirality : 0.042 0.136 535 Planarity : 0.004 0.035 603 Dihedral : 5.349 46.741 582 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 1.64 % Allowed : 13.93 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.41), residues: 421 helix: -1.78 (1.13), residues: 20 sheet: -0.53 (0.43), residues: 153 loop : -0.97 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 55 TYR 0.034 0.001 TYR L 49 PHE 0.008 0.001 PHE H 64 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 3488) covalent geometry : angle 0.51233 / 0.27 ( 4747) SS BOND : bond 0.00145 / 0.07 ( 6) SS BOND : angle 0.75608 / 0.37 ( 12) hydrogen bonds : bond 0.02779 / 1.84 ( 99) hydrogen bonds : angle 5.43010 / 3.85 ( 264) link_ALPHA1-3 : bond 0.00919 / 0.48 ( 1) link_ALPHA1-3 : angle 2.28180 / 1.24 ( 3) link_ALPHA1-6 : bond 0.00407 / 0.21 ( 1) link_ALPHA1-6 : angle 1.50451 / 0.80 ( 3) link_BETA1-4 : bond 0.00303 / 0.15 ( 2) link_BETA1-4 : angle 1.49176 / 0.74 ( 6) link_BETA1-6 : bond 0.00195 / 0.10 ( 1) link_BETA1-6 : angle 1.31786 / 0.63 ( 3) link_NAG-ASN : bond 0.00059 / 0.03 ( 1) link_NAG-ASN : angle 2.36952 / 1.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9346 (tt0) cc_final: 0.9041 (tm-30) REVERT: G 378 LYS cc_start: 0.9156 (ttmm) cc_final: 0.8647 (ptmm) REVERT: G 414 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8714 (tp40) REVERT: G 427 ASP cc_start: 0.8800 (m-30) cc_final: 0.8532 (p0) REVERT: H 62 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8607 (tm-30) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.1550 time to fit residues: 11.3293 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 409 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 = 0.2995 r_free = 0.2995 target = 0.059322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.048347 restraints weight = 35060.238| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 4.30 r_work: 0.2606 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3500 Z= 0.264 Angle : 0.575 4.560 4777 Z= 0.300 Chirality : 0.042 0.134 535 Planarity : 0.005 0.046 603 Dihedral : 5.449 46.549 582 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 2.19 % Allowed : 13.66 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.40), residues: 421 helix: -1.95 (1.09), residues: 20 sheet: -0.72 (0.42), residues: 153 loop : -1.13 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 97 TYR 0.023 0.002 TYR L 49 PHE 0.009 0.001 PHE H 64 TRP 0.007 0.001 TRP H 110 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 ( 3488) covalent geometry : angle 0.56134 / 0.30 ( 4747) SS BOND : bond 0.00156 / 0.07 ( 6) SS BOND : angle 0.85838 / 0.45 ( 12) hydrogen bonds : bond 0.03211 / 2.11 ( 99) hydrogen bonds : angle 5.59932 / 3.94 ( 264) link_ALPHA1-3 : bond 0.00695 / 0.37 ( 1) link_ALPHA1-3 : angle 2.71673 / 1.48 ( 3) link_ALPHA1-6 : bond 0.00323 / 0.17 ( 1) link_ALPHA1-6 : angle 1.59815 / 0.86 ( 3) link_BETA1-4 : bond 0.00400 / 0.20 ( 2) link_BETA1-4 : angle 1.60981 / 0.77 ( 6) link_BETA1-6 : bond 0.00144 / 0.08 ( 1) link_BETA1-6 : angle 1.37100 / 0.62 ( 3) link_NAG-ASN : bond 0.00148 / 0.08 ( 1) link_NAG-ASN : angle 2.78943 / 1.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9372 (tt0) cc_final: 0.9079 (tm-30) REVERT: G 378 LYS cc_start: 0.9191 (ttmm) cc_final: 0.8681 (ptmm) REVERT: G 427 ASP cc_start: 0.8777 (m-30) cc_final: 0.8544 (p0) REVERT: H 62 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8644 (tm-30) REVERT: H 99 HIS cc_start: 0.9390 (OUTLIER) cc_final: 0.8557 (t-90) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1579 time to fit residues: 11.3038 Evaluate side-chains 61 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3007 r_free = 0.3007 target = 0.058368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.048271 restraints weight = 33783.174| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 4.17 r_work: 0.2639 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3500 Z= 0.124 Angle : 0.543 5.204 4777 Z= 0.284 Chirality : 0.042 0.151 535 Planarity : 0.004 0.053 603 Dihedral : 5.294 47.320 582 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 1.91 % Allowed : 14.48 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.41), residues: 421 helix: -1.71 (1.16), residues: 20 sheet: -0.53 (0.43), residues: 153 loop : -1.03 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 97 TYR 0.029 0.001 TYR L 49 PHE 0.009 0.001 PHE H 64 TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 3488) covalent geometry : angle 0.53317 / 0.28 ( 4747) SS BOND : bond 0.00176 / 0.08 ( 6) SS BOND : angle 0.78556 / 0.37 ( 12) hydrogen bonds : bond 0.02818 / 1.88 ( 99) hydrogen bonds : angle 5.48707 / 3.89 ( 264) link_ALPHA1-3 : bond 0.00792 / 0.42 ( 1) link_ALPHA1-3 : angle 2.10580 / 1.15 ( 3) link_ALPHA1-6 : bond 0.00412 / 0.22 ( 1) link_ALPHA1-6 : angle 1.47947 / 0.79 ( 3) link_BETA1-4 : bond 0.00286 / 0.14 ( 2) link_BETA1-4 : angle 1.53887 / 0.78 ( 6) link_BETA1-6 : bond 0.00149 / 0.08 ( 1) link_BETA1-6 : angle 1.26447 / 0.60 ( 3) link_NAG-ASN : bond 0.00106 / 0.06 ( 1) link_NAG-ASN : angle 2.26222 / 1.31 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9340 (tt0) cc_final: 0.9065 (tm-30) REVERT: G 378 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8682 (ptmm) REVERT: G 414 GLN cc_start: 0.9054 (tp40) cc_final: 0.8839 (tp-100) REVERT: G 427 ASP cc_start: 0.8749 (m-30) cc_final: 0.8512 (p0) REVERT: H 62 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8642 (tm-30) REVERT: H 99 HIS cc_start: 0.9356 (OUTLIER) cc_final: 0.8590 (t-90) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.1741 time to fit residues: 12.8395 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3006 r_free = 0.3006 target = 0.059736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048940 restraints weight = 34355.215| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 4.26 r_work: 0.2583 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3500 Z= 0.195 Angle : 0.559 4.873 4777 Z= 0.290 Chirality : 0.042 0.137 535 Planarity : 0.004 0.050 603 Dihedral : 5.285 46.700 582 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 2.19 % Allowed : 13.93 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.44 (0.41), residues: 421 helix: -1.81 (1.12), residues: 20 sheet: -0.59 (0.43), residues: 153 loop : -1.10 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 97 TYR 0.026 0.001 TYR L 49 PHE 0.008 0.001 PHE H 64 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 3488) covalent geometry : angle 0.54725 / 0.29 ( 4747) SS BOND : bond 0.00163 / 0.07 ( 6) SS BOND : angle 0.78534 / 0.38 ( 12) hydrogen bonds : bond 0.02938 / 1.93 ( 99) hydrogen bonds : angle 5.54150 / 3.92 ( 264) link_ALPHA1-3 : bond 0.00645 / 0.34 ( 1) link_ALPHA1-3 : angle 2.28758 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00390 / 0.21 ( 1) link_ALPHA1-6 : angle 1.55108 / 0.83 ( 3) link_BETA1-4 : bond 0.00305 / 0.15 ( 2) link_BETA1-4 : angle 1.51917 / 0.75 ( 6) link_BETA1-6 : bond 0.00136 / 0.07 ( 1) link_BETA1-6 : angle 1.39230 / 0.65 ( 3) link_NAG-ASN : bond 0.00068 / 0.04 ( 1) link_NAG-ASN : angle 2.57970 / 1.48 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.92 seconds wall clock time: 29 minutes 58.88 seconds (1798.88 seconds total)