Starting phenix.real_space_refine on Thu Jul 2 06:31:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyc_18750/07_2026/8qyc_18750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyc_18750/07_2026/8qyc_18750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyc_18750/07_2026/8qyc_18750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyc_18750/07_2026/8qyc_18750.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyc_18750/07_2026/8qyc_18750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyc_18750/07_2026/8qyc_18750.cif" } resolution = 2.75 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= 0.110 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 P 3 5.49 5 S 16 5.16 5 C 4592 2.51 5 N 1246 2.21 5 O 1341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7167 Classifications: {'peptide': 893} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 50, 'TRANS': 842} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.21 Number of scatterers: 7198 At special positions: 0 Unit cell: (83.2, 119.808, 94.848, 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 16 16.00 P 3 15.00 O 1341 8.00 N 1246 7.00 C 4592 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=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 435.0 milliseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 9 sheets defined 49.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.579A pdb=" N ILE A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 188 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.623A pdb=" N SER A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.768A pdb=" N VAL A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.234A pdb=" N PHE A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.192A pdb=" N SER A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 360 through 377 removed outlier: 3.813A pdb=" N LEU A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'A' and resid 581 through 596 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.774A pdb=" N ASN A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 675 Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 765 through 777 removed outlier: 4.250A pdb=" N LEU A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 844 through 864 Processing helix chain 'A' and resid 875 through 888 Processing helix chain 'A' and resid 888 through 893 removed outlier: 3.921A pdb=" N VAL A 892 " --> pdb=" O HIS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 902 through 919 Processing helix chain 'A' and resid 929 through 945 Processing helix chain 'A' and resid 958 through 975 removed outlier: 4.861A pdb=" N SER A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1017 Processing helix chain 'A' and resid 1042 through 1059 Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1075 through 1079 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.716A pdb=" N ARG A 65 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104 removed outlier: 6.195A pdb=" N SER A 102 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE A 116 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ARG A 104 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A 114 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP A 119 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 201 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 213 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.076A pdb=" N GLU A 338 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 663 through 665 removed outlier: 6.440A pdb=" N LEU A 664 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 725 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS A 605 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N LEU A 818 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 606 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 834 removed outlier: 6.900A pdb=" N ASN A 998 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR A1031 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A1000 " --> pdb=" O TYR A1031 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS A 922 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 949 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 841 through 842 removed outlier: 5.937A pdb=" N LEU A 841 " --> pdb=" O ARG A1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 355 hydrogen bonds defined for protein. 1008 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: 1.14 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 2485 1.37 - 1.52: 2245 1.52 - 1.66: 2616 1.66 - 1.80: 13 1.80 - 1.95: 8 Bond restraints: 7367 Sorted by residual: bond pdb=" O3B AGS A1101 " pdb=" PB AGS A1101 " ideal model delta sigma weight residual 1.673 1.587 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" O3A AGS A1101 " pdb=" PA AGS A1101 " ideal model delta sigma weight residual 1.664 1.587 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" O3B AGS A1101 " pdb=" PG AGS A1101 " ideal model delta sigma weight residual 1.614 1.561 0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" O5' AGS A1101 " pdb=" PA AGS A1101 " ideal model delta sigma weight residual 1.634 1.584 0.050 2.00e-02 2.50e+03 6.30e+00 bond pdb=" O2G AGS A1101 " pdb=" PG AGS A1101 " ideal model delta sigma weight residual 1.604 1.557 0.047 2.00e-02 2.50e+03 5.62e+00 ... (remaining 7362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 9921 1.96 - 3.93: 84 3.93 - 5.89: 12 5.89 - 7.85: 1 7.85 - 9.82: 6 Bond angle restraints: 10024 Sorted by residual: angle pdb=" O3A AGS A1101 " pdb=" PB AGS A1101 " pdb=" O3B AGS A1101 " ideal model delta sigma weight residual 100.38 110.20 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3A AGS A1101 " pdb=" PA AGS A1101 " pdb=" O5' AGS A1101 " ideal model delta sigma weight residual 97.67 106.73 -9.06 3.00e+00 1.11e-01 9.11e+00 angle pdb=" PB AGS A1101 " pdb=" O3B AGS A1101 " pdb=" PG AGS A1101 " ideal model delta sigma weight residual 129.21 120.39 8.82 3.00e+00 1.11e-01 8.64e+00 angle pdb=" O1B AGS A1101 " pdb=" PB AGS A1101 " pdb=" O2B AGS A1101 " ideal model delta sigma weight residual 121.53 112.89 8.64 3.00e+00 1.11e-01 8.30e+00 angle pdb=" O1A AGS A1101 " pdb=" PA AGS A1101 " pdb=" O2A AGS A1101 " ideal model delta sigma weight residual 122.09 113.84 8.25 3.00e+00 1.11e-01 7.56e+00 ... (remaining 10019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4216 17.43 - 34.86: 188 34.86 - 52.29: 42 52.29 - 69.72: 13 69.72 - 87.15: 7 Dihedral angle restraints: 4466 sinusoidal: 1854 harmonic: 2612 Sorted by residual: dihedral pdb=" CA PHE A 130 " pdb=" C PHE A 130 " pdb=" N SER A 131 " pdb=" CA SER A 131 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP A1017 " pdb=" C ASP A1017 " pdb=" N ARG A1018 " pdb=" CA ARG A1018 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" N LEU A 620 " pdb=" CA LEU A 620 " pdb=" CB LEU A 620 " pdb=" CG LEU A 620 " ideal model delta sinusoidal sigma weight residual -60.00 -119.63 59.63 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 967 0.054 - 0.108: 126 0.108 - 0.162: 27 0.162 - 0.215: 0 0.215 - 0.269: 1 Chirality restraints: 1121 Sorted by residual: chirality pdb=" C3' AGS A1101 " pdb=" C2' AGS A1101 " pdb=" C4' AGS A1101 " pdb=" O3' AGS A1101 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ILE A 681 " pdb=" N ILE A 681 " pdb=" C ILE A 681 " pdb=" CB ILE A 681 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA VAL A 91 " pdb=" N VAL A 91 " pdb=" C VAL A 91 " pdb=" CB VAL A 91 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1118 not shown) Planarity restraints: 1294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 598 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO A 599 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 599 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 599 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 893 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 894 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 894 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 894 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 681 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 682 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " -0.017 5.00e-02 4.00e+02 ... (remaining 1291 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 182 2.71 - 3.26: 6996 3.26 - 3.80: 11977 3.80 - 4.35: 15869 4.35 - 4.90: 26231 Nonbonded interactions: 61255 Sorted by model distance: nonbonded pdb=" O1A AGS A1101 " pdb=" O2B AGS A1101 " model vdw 2.161 3.040 nonbonded pdb=" O HIS A 583 " pdb=" NH1 ARG A 820 " model vdw 2.257 3.120 nonbonded pdb=" OD1 ASP A 646 " pdb=" NZ LYS A 665 " model vdw 2.283 3.120 nonbonded pdb=" NZ LYS A 904 " pdb=" OE2 GLU A1044 " model vdw 2.300 3.120 nonbonded pdb=" O VAL A 244 " pdb=" NZ LYS A 267 " model vdw 2.304 3.120 ... (remaining 61250 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 0.086 7367 Z= 0.144 Angle : 0.515 9.817 10024 Z= 0.250 Chirality : 0.041 0.269 1121 Planarity : 0.004 0.048 1294 Dihedral : 11.547 87.151 2760 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.29 % Allowed : 3.21 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 885 helix: 1.70 (0.27), residues: 381 sheet: 0.54 (0.45), residues: 123 loop : -0.01 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 897 TYR 0.010 0.001 TYR A 676 PHE 0.010 0.001 PHE A 622 TRP 0.015 0.001 TRP A 177 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 7367) covalent geometry : angle 0.51498 / 0.25 (10024) hydrogen bonds : bond 0.16904 / 10.85 ( 355) hydrogen bonds : angle 6.74150 / 4.61 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.278 Fit side-chains REVERT: A 109 ASP cc_start: 0.7004 (m-30) cc_final: 0.6792 (m-30) REVERT: A 118 GLU cc_start: 0.7227 (pt0) cc_final: 0.6939 (pt0) REVERT: A 222 GLU cc_start: 0.7079 (pp20) cc_final: 0.6875 (tm-30) REVERT: A 268 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6400 (pt0) REVERT: A 369 GLN cc_start: 0.7867 (mm110) cc_final: 0.7507 (mm110) REVERT: A 790 GLN cc_start: 0.7181 (tt0) cc_final: 0.6896 (tt0) REVERT: A 942 GLN cc_start: 0.7773 (mt0) cc_final: 0.7570 (mt0) REVERT: A 970 ASP cc_start: 0.7183 (m-30) cc_final: 0.6753 (m-30) REVERT: A 993 ASN cc_start: 0.8058 (p0) cc_final: 0.7856 (p0) REVERT: A 996 LYS cc_start: 0.7483 (mmtp) cc_final: 0.6852 (mptt) REVERT: A 1014 GLN cc_start: 0.7931 (mm110) cc_final: 0.7519 (tp40) REVERT: A 1018 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.7719 (mmp-170) outliers start: 10 outliers final: 1 residues processed: 149 average time/residue: 0.5780 time to fit residues: 90.3893 Evaluate side-chains 110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN A 259 HIS A 312 GLN A 995 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN A1052 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.166932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.136394 restraints weight = 7627.860| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.75 r_work: 0.3447 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7367 Z= 0.152 Angle : 0.514 6.683 10024 Z= 0.267 Chirality : 0.043 0.210 1121 Planarity : 0.004 0.049 1294 Dihedral : 6.655 49.226 994 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.93 % Allowed : 10.03 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.29), residues: 885 helix: 1.62 (0.27), residues: 385 sheet: 0.52 (0.44), residues: 123 loop : -0.01 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 104 TYR 0.012 0.002 TYR A 294 PHE 0.011 0.002 PHE A 978 TRP 0.015 0.002 TRP A 177 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7367) covalent geometry : angle 0.51360 / 0.27 (10024) hydrogen bonds : bond 0.04399 / 2.77 ( 355) hydrogen bonds : angle 5.10468 / 3.54 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.314 Fit side-chains REVERT: A 80 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: A 104 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7397 (ptt90) REVERT: A 222 GLU cc_start: 0.6926 (pp20) cc_final: 0.6701 (tm-30) REVERT: A 280 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7848 (mtm110) REVERT: A 369 GLN cc_start: 0.7964 (mm110) cc_final: 0.7632 (mm110) REVERT: A 647 ASN cc_start: 0.8051 (t0) cc_final: 0.7815 (t0) REVERT: A 827 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7655 (pmm-80) REVERT: A 970 ASP cc_start: 0.7381 (m-30) cc_final: 0.6914 (m-30) REVERT: A 996 LYS cc_start: 0.7719 (mmtp) cc_final: 0.7158 (mptt) outliers start: 15 outliers final: 6 residues processed: 134 average time/residue: 0.6084 time to fit residues: 85.6363 Evaluate side-chains 118 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 0.0010 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN A 995 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129374 restraints weight = 7715.577| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.03 r_work: 0.3374 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7367 Z= 0.129 Angle : 0.488 5.951 10024 Z= 0.253 Chirality : 0.042 0.209 1121 Planarity : 0.004 0.045 1294 Dihedral : 6.571 53.229 994 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.21 % Allowed : 10.93 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.29), residues: 885 helix: 1.76 (0.27), residues: 386 sheet: -0.12 (0.43), residues: 133 loop : 0.13 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1059 TYR 0.015 0.002 TYR A 667 PHE 0.014 0.001 PHE A 898 TRP 0.015 0.001 TRP A 177 HIS 0.003 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7367) covalent geometry : angle 0.48803 / 0.25 (10024) hydrogen bonds : bond 0.03877 / 2.45 ( 355) hydrogen bonds : angle 4.78305 / 3.31 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.225 Fit side-chains REVERT: A 80 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: A 104 ARG cc_start: 0.7511 (ptt90) cc_final: 0.7237 (ptt90) REVERT: A 280 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7503 (mtm110) REVERT: A 369 GLN cc_start: 0.7683 (mm110) cc_final: 0.7271 (mm110) REVERT: A 654 ASN cc_start: 0.6875 (m-40) cc_final: 0.6638 (m-40) REVERT: A 710 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: A 790 GLN cc_start: 0.7046 (tt0) cc_final: 0.6549 (mm-40) REVERT: A 805 ARG cc_start: 0.6717 (mmp-170) cc_final: 0.6053 (mmp-170) REVERT: A 827 ARG cc_start: 0.7851 (ptp-170) cc_final: 0.7419 (pmm-80) REVERT: A 970 ASP cc_start: 0.6828 (m-30) cc_final: 0.6316 (m-30) outliers start: 25 outliers final: 10 residues processed: 124 average time/residue: 0.5753 time to fit residues: 75.1805 Evaluate side-chains 114 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 837 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 61 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 166 GLN A 995 GLN ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128631 restraints weight = 7873.056| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.07 r_work: 0.3363 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7367 Z= 0.136 Angle : 0.491 6.149 10024 Z= 0.254 Chirality : 0.042 0.225 1121 Planarity : 0.004 0.047 1294 Dihedral : 6.634 57.073 994 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.86 % Allowed : 11.44 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.29), residues: 885 helix: 1.80 (0.27), residues: 385 sheet: -0.26 (0.42), residues: 133 loop : 0.11 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1059 TYR 0.013 0.002 TYR A 294 PHE 0.016 0.001 PHE A 898 TRP 0.016 0.001 TRP A 177 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7367) covalent geometry : angle 0.49125 / 0.25 (10024) hydrogen bonds : bond 0.03773 / 2.38 ( 355) hydrogen bonds : angle 4.62703 / 3.19 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.211 Fit side-chains REVERT: A 65 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6807 (ttp-170) REVERT: A 80 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: A 104 ARG cc_start: 0.7461 (ptt90) cc_final: 0.7156 (ptt90) REVERT: A 181 ARG cc_start: 0.7283 (ttt90) cc_final: 0.6991 (ttt90) REVERT: A 223 ILE cc_start: 0.8285 (mt) cc_final: 0.8054 (mp) REVERT: A 271 ASN cc_start: 0.7987 (m-40) cc_final: 0.7570 (m-40) REVERT: A 280 ARG cc_start: 0.7745 (mtm180) cc_final: 0.7528 (mtm110) REVERT: A 369 GLN cc_start: 0.7702 (mm110) cc_final: 0.7235 (mm110) REVERT: A 586 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: A 611 MET cc_start: 0.7896 (tpp) cc_final: 0.7598 (mmp) REVERT: A 647 ASN cc_start: 0.7576 (t0) cc_final: 0.7289 (t0) REVERT: A 710 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: A 790 GLN cc_start: 0.7145 (tt0) cc_final: 0.6705 (mm-40) REVERT: A 805 ARG cc_start: 0.6733 (mmp-170) cc_final: 0.6069 (mmp-170) REVERT: A 827 ARG cc_start: 0.7915 (ptp-170) cc_final: 0.7444 (pmm-80) REVERT: A 970 ASP cc_start: 0.6861 (m-30) cc_final: 0.6327 (m-30) REVERT: A 1048 ASP cc_start: 0.7346 (t70) cc_final: 0.7123 (t70) outliers start: 30 outliers final: 13 residues processed: 121 average time/residue: 0.5033 time to fit residues: 64.4149 Evaluate side-chains 117 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 166 GLN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.159134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126614 restraints weight = 7845.514| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.03 r_work: 0.3342 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7367 Z= 0.179 Angle : 0.537 7.106 10024 Z= 0.276 Chirality : 0.044 0.252 1121 Planarity : 0.004 0.047 1294 Dihedral : 6.756 58.172 994 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.47 % Allowed : 12.34 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.28), residues: 885 helix: 1.63 (0.26), residues: 385 sheet: 0.07 (0.42), residues: 127 loop : -0.06 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 325 TYR 0.014 0.002 TYR A 294 PHE 0.017 0.002 PHE A 898 TRP 0.017 0.002 TRP A 177 HIS 0.005 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 7367) covalent geometry : angle 0.53709 / 0.28 (10024) hydrogen bonds : bond 0.04113 / 2.58 ( 355) hydrogen bonds : angle 4.72434 / 3.26 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.290 Fit side-chains REVERT: A 65 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6911 (ttp-170) REVERT: A 80 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: A 280 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7599 (mtm110) REVERT: A 369 GLN cc_start: 0.7726 (mm110) cc_final: 0.7319 (mm110) REVERT: A 586 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6470 (tm-30) REVERT: A 647 ASN cc_start: 0.7499 (t0) cc_final: 0.7228 (t0) REVERT: A 710 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: A 827 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7571 (pmm-80) REVERT: A 970 ASP cc_start: 0.6891 (m-30) cc_final: 0.6327 (m-30) REVERT: A 1048 ASP cc_start: 0.7479 (t70) cc_final: 0.7168 (t70) outliers start: 27 outliers final: 14 residues processed: 122 average time/residue: 0.4941 time to fit residues: 63.6865 Evaluate side-chains 122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 998 ASN Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 166 GLN A 790 GLN A 973 GLN ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129168 restraints weight = 7816.061| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.04 r_work: 0.3382 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7367 Z= 0.123 Angle : 0.479 5.723 10024 Z= 0.248 Chirality : 0.042 0.260 1121 Planarity : 0.004 0.045 1294 Dihedral : 6.536 58.005 994 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.70 % Allowed : 13.62 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 885 helix: 1.99 (0.27), residues: 378 sheet: -0.34 (0.42), residues: 137 loop : 0.13 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 104 TYR 0.013 0.001 TYR A 294 PHE 0.017 0.001 PHE A 898 TRP 0.018 0.001 TRP A 177 HIS 0.003 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7367) covalent geometry : angle 0.47908 / 0.25 (10024) hydrogen bonds : bond 0.03589 / 2.26 ( 355) hydrogen bonds : angle 4.49903 / 3.10 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.262 Fit side-chains REVERT: A 80 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: A 271 ASN cc_start: 0.8007 (m-40) cc_final: 0.7652 (m-40) REVERT: A 369 GLN cc_start: 0.7715 (mm110) cc_final: 0.7248 (mm110) REVERT: A 586 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: A 647 ASN cc_start: 0.7572 (t0) cc_final: 0.7298 (t0) REVERT: A 710 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: A 819 ARG cc_start: 0.8444 (tpt170) cc_final: 0.8233 (tpt90) REVERT: A 827 ARG cc_start: 0.7916 (ptp-170) cc_final: 0.7540 (pmm-80) REVERT: A 970 ASP cc_start: 0.6857 (m-30) cc_final: 0.6335 (m-30) REVERT: A 1048 ASP cc_start: 0.7481 (t70) cc_final: 0.7138 (t70) outliers start: 21 outliers final: 14 residues processed: 115 average time/residue: 0.5192 time to fit residues: 62.7738 Evaluate side-chains 114 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 998 ASN Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 66 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.0070 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 166 GLN A 790 GLN A 831 GLN A1052 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.160312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127850 restraints weight = 7812.816| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.05 r_work: 0.3357 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7367 Z= 0.148 Angle : 0.505 6.259 10024 Z= 0.261 Chirality : 0.043 0.278 1121 Planarity : 0.004 0.047 1294 Dihedral : 6.490 54.839 994 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.34 % Allowed : 13.88 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 885 helix: 1.91 (0.26), residues: 378 sheet: 0.04 (0.43), residues: 127 loop : -0.04 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 325 TYR 0.014 0.001 TYR A 294 PHE 0.018 0.002 PHE A 898 TRP 0.017 0.002 TRP A 177 HIS 0.004 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7367) covalent geometry : angle 0.50532 / 0.26 (10024) hydrogen bonds : bond 0.03796 / 2.38 ( 355) hydrogen bonds : angle 4.52614 / 3.11 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.267 Fit side-chains REVERT: A 65 ARG cc_start: 0.7054 (ttp-170) cc_final: 0.6766 (ttp-170) REVERT: A 80 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: A 181 ARG cc_start: 0.7208 (ttt90) cc_final: 0.6940 (ttt90) REVERT: A 223 ILE cc_start: 0.8006 (pt) cc_final: 0.7715 (tt) REVERT: A 271 ASN cc_start: 0.7986 (m-40) cc_final: 0.7577 (m-40) REVERT: A 369 GLN cc_start: 0.7695 (mm110) cc_final: 0.7217 (mm110) REVERT: A 586 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6440 (tm-30) REVERT: A 647 ASN cc_start: 0.7552 (t0) cc_final: 0.7269 (t0) REVERT: A 710 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: A 819 ARG cc_start: 0.8475 (tpt170) cc_final: 0.8248 (tpt90) REVERT: A 827 ARG cc_start: 0.7945 (ptp-170) cc_final: 0.7561 (pmm-80) REVERT: A 970 ASP cc_start: 0.6814 (m-30) cc_final: 0.6254 (m-30) REVERT: A 1048 ASP cc_start: 0.7462 (t70) cc_final: 0.7105 (t70) outliers start: 26 outliers final: 16 residues processed: 119 average time/residue: 0.5196 time to fit residues: 64.9998 Evaluate side-chains 122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 998 ASN Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.0870 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.0030 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN A 790 GLN A 995 GLN A1052 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130339 restraints weight = 7829.679| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.04 r_work: 0.3378 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7367 Z= 0.111 Angle : 0.470 4.980 10024 Z= 0.244 Chirality : 0.042 0.303 1121 Planarity : 0.004 0.042 1294 Dihedral : 6.244 52.974 994 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.70 % Allowed : 14.91 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 885 helix: 2.04 (0.26), residues: 379 sheet: -0.35 (0.43), residues: 138 loop : 0.12 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 104 TYR 0.013 0.001 TYR A 294 PHE 0.009 0.001 PHE A 898 TRP 0.018 0.001 TRP A 177 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 7367) covalent geometry : angle 0.46998 / 0.24 (10024) hydrogen bonds : bond 0.03468 / 2.18 ( 355) hydrogen bonds : angle 4.35765 / 3.00 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.203 Fit side-chains REVERT: A 65 ARG cc_start: 0.6994 (ttp-170) cc_final: 0.6748 (ttp-170) REVERT: A 80 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6589 (tm-30) REVERT: A 104 ARG cc_start: 0.7539 (ptt90) cc_final: 0.7329 (ptt90) REVERT: A 181 ARG cc_start: 0.7199 (ttt90) cc_final: 0.6927 (ttt90) REVERT: A 271 ASN cc_start: 0.7867 (m-40) cc_final: 0.7516 (m-40) REVERT: A 369 GLN cc_start: 0.7670 (mm110) cc_final: 0.7210 (mm110) REVERT: A 586 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6457 (tm-30) REVERT: A 710 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: A 819 ARG cc_start: 0.8405 (tpt170) cc_final: 0.8196 (tpt90) REVERT: A 827 ARG cc_start: 0.7921 (ptp-170) cc_final: 0.7551 (pmm-80) REVERT: A 970 ASP cc_start: 0.6897 (m-30) cc_final: 0.6364 (m-30) REVERT: A 1048 ASP cc_start: 0.7424 (t70) cc_final: 0.7102 (t70) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.5580 time to fit residues: 65.2412 Evaluate side-chains 113 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 998 ASN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN A 790 GLN A 995 GLN A1052 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.161155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128646 restraints weight = 7783.093| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.05 r_work: 0.3378 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7367 Z= 0.134 Angle : 0.494 5.616 10024 Z= 0.255 Chirality : 0.043 0.304 1121 Planarity : 0.004 0.048 1294 Dihedral : 6.174 49.327 994 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.31 % Allowed : 15.30 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.29), residues: 885 helix: 1.92 (0.26), residues: 379 sheet: -0.11 (0.42), residues: 133 loop : 0.02 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 325 TYR 0.013 0.001 TYR A 294 PHE 0.010 0.001 PHE A 773 TRP 0.017 0.001 TRP A 177 HIS 0.003 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7367) covalent geometry : angle 0.49421 / 0.26 (10024) hydrogen bonds : bond 0.03647 / 2.29 ( 355) hydrogen bonds : angle 4.41308 / 3.04 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.248 Fit side-chains REVERT: A 65 ARG cc_start: 0.7040 (ttp-170) cc_final: 0.6815 (ttp-170) REVERT: A 80 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6628 (tm-30) REVERT: A 104 ARG cc_start: 0.7584 (ptt90) cc_final: 0.7351 (ptt90) REVERT: A 181 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6935 (ttt90) REVERT: A 271 ASN cc_start: 0.7918 (m-40) cc_final: 0.7569 (m-40) REVERT: A 369 GLN cc_start: 0.7683 (mm110) cc_final: 0.7213 (mm110) REVERT: A 586 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: A 710 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: A 819 ARG cc_start: 0.8458 (tpt170) cc_final: 0.8223 (tpt90) REVERT: A 823 GLU cc_start: 0.6764 (pp20) cc_final: 0.6160 (mm-30) REVERT: A 827 ARG cc_start: 0.7943 (ptp-170) cc_final: 0.7569 (pmm-80) REVERT: A 970 ASP cc_start: 0.6853 (m-30) cc_final: 0.6332 (m-30) REVERT: A 1048 ASP cc_start: 0.7481 (t70) cc_final: 0.7111 (t70) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.5943 time to fit residues: 69.3506 Evaluate side-chains 115 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 998 ASN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 63 optimal weight: 0.0980 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN A 790 GLN A 995 GLN A1052 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.163004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130765 restraints weight = 7730.666| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.04 r_work: 0.3386 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7367 Z= 0.109 Angle : 0.474 4.872 10024 Z= 0.246 Chirality : 0.042 0.304 1121 Planarity : 0.004 0.041 1294 Dihedral : 5.959 46.688 994 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.19 % Allowed : 15.81 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.29), residues: 885 helix: 2.04 (0.26), residues: 379 sheet: -0.49 (0.42), residues: 144 loop : 0.21 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 325 TYR 0.012 0.001 TYR A 294 PHE 0.008 0.001 PHE A 773 TRP 0.018 0.001 TRP A 177 HIS 0.003 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7367) covalent geometry : angle 0.47402 / 0.25 (10024) hydrogen bonds : bond 0.03390 / 2.13 ( 355) hydrogen bonds : angle 4.31798 / 2.96 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.269 Fit side-chains REVERT: A 80 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: A 104 ARG cc_start: 0.7573 (ptt90) cc_final: 0.7354 (ptt90) REVERT: A 181 ARG cc_start: 0.7233 (ttt90) cc_final: 0.6968 (ttt90) REVERT: A 271 ASN cc_start: 0.7829 (m-40) cc_final: 0.7479 (m-40) REVERT: A 369 GLN cc_start: 0.7686 (mm110) cc_final: 0.7225 (mm110) REVERT: A 586 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: A 710 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: A 819 ARG cc_start: 0.8386 (tpt170) cc_final: 0.8172 (tpt90) REVERT: A 823 GLU cc_start: 0.6652 (pp20) cc_final: 0.6087 (mm-30) REVERT: A 827 ARG cc_start: 0.7933 (ptp-170) cc_final: 0.7571 (pmm-80) REVERT: A 970 ASP cc_start: 0.6890 (m-30) cc_final: 0.6359 (m-30) REVERT: A 1048 ASP cc_start: 0.7304 (t70) cc_final: 0.6915 (t70) outliers start: 17 outliers final: 13 residues processed: 114 average time/residue: 0.5891 time to fit residues: 70.5003 Evaluate side-chains 118 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 998 ASN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN A 654 ASN A 790 GLN A1052 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.161702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129214 restraints weight = 7857.856| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.06 r_work: 0.3369 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7367 Z= 0.129 Angle : 0.496 5.315 10024 Z= 0.257 Chirality : 0.042 0.304 1121 Planarity : 0.004 0.047 1294 Dihedral : 5.927 49.686 994 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.57 % Allowed : 15.94 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.29), residues: 885 helix: 1.96 (0.26), residues: 379 sheet: -0.48 (0.42), residues: 144 loop : 0.17 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 325 TYR 0.013 0.001 TYR A 294 PHE 0.010 0.001 PHE A 773 TRP 0.017 0.001 TRP A 177 HIS 0.004 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7367) covalent geometry : angle 0.49572 / 0.26 (10024) hydrogen bonds : bond 0.03580 / 2.24 ( 355) hydrogen bonds : angle 4.39244 / 3.01 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.56 seconds wall clock time: 43 minutes 32.11 seconds (2612.11 seconds total)