Starting phenix.real_space_refine on Tue Jan 14 19:57:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyc_18750/01_2025/8qyc_18750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyc_18750/01_2025/8qyc_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_18750/01_2025/8qyc_18750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyc_18750/01_2025/8qyc_18750.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyc_18750/01_2025/8qyc_18750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyc_18750/01_2025/8qyc_18750.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.60, per 1000 atoms: 0.78 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: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.02 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: 2.74 Time building geometry restraints manager: 2.04 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=" C4' AGS A1101 " pdb=" O4' AGS A1101 " ideal model delta sigma weight residual 1.444 1.435 0.009 1.20e-02 6.94e+03 6.09e-01 bond pdb=" C SER A 598 " pdb=" N PRO A 599 " ideal model delta sigma weight residual 1.336 1.345 -0.009 1.20e-02 6.94e+03 5.06e-01 bond pdb=" C2' AGS A1101 " pdb=" C3' AGS A1101 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.30e-02 5.92e+03 4.62e-01 bond pdb=" CA VAL A 994 " pdb=" CB VAL A 994 " ideal model delta sigma weight residual 1.532 1.539 -0.007 1.08e-02 8.57e+03 4.29e-01 bond pdb=" CA ILE A 982 " pdb=" CB ILE A 982 " ideal model delta sigma weight residual 1.540 1.531 0.009 1.36e-02 5.41e+03 4.04e-01 ... (remaining 7362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 9778 1.13 - 2.26: 179 2.26 - 3.39: 53 3.39 - 4.52: 12 4.52 - 5.65: 2 Bond angle restraints: 10024 Sorted by residual: angle pdb=" N SER A 598 " pdb=" CA SER A 598 " pdb=" C SER A 598 " ideal model delta sigma weight residual 109.81 114.31 -4.50 2.21e+00 2.05e-01 4.15e+00 angle pdb=" CA TRP A 177 " pdb=" CB TRP A 177 " pdb=" CG TRP A 177 " ideal model delta sigma weight residual 113.60 109.75 3.85 1.90e+00 2.77e-01 4.11e+00 angle pdb=" C1' AGS A1101 " pdb=" C2' AGS A1101 " pdb=" C3' AGS A1101 " ideal model delta sigma weight residual 101.46 103.84 -2.38 1.19e+00 7.12e-01 4.05e+00 angle pdb=" N ASP A 828 " pdb=" CA ASP A 828 " pdb=" C ASP A 828 " ideal model delta sigma weight residual 111.81 109.00 2.81 1.44e+00 4.82e-01 3.81e+00 angle pdb=" C LEU A 809 " pdb=" N ARG A 810 " pdb=" CA ARG A 810 " ideal model delta sigma weight residual 120.31 123.18 -2.87 1.52e+00 4.33e-01 3.57e+00 ... (remaining 10019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4214 17.43 - 34.86: 181 34.86 - 52.29: 38 52.29 - 69.72: 9 69.72 - 87.15: 6 Dihedral angle restraints: 4448 sinusoidal: 1836 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 4445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 757 0.031 - 0.063: 250 0.063 - 0.094: 49 0.094 - 0.125: 63 0.125 - 0.157: 4 Chirality restraints: 1123 Sorted by residual: 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 chirality pdb=" CA ILE A 570 " pdb=" N ILE A 570 " pdb=" C ILE A 570 " pdb=" CB ILE A 570 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1120 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.002 0.019 7367 Z= 0.150 Angle : 0.443 5.653 10024 Z= 0.237 Chirality : 0.040 0.157 1123 Planarity : 0.004 0.048 1294 Dihedral : 11.072 87.151 2742 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP A 177 HIS 0.002 0.001 HIS A 274 PHE 0.010 0.001 PHE A 622 TYR 0.010 0.001 TYR A 676 ARG 0.003 0.000 ARG A 897 *********************** 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 : 0.825 Fit side-chains REVERT: A 109 ASP cc_start: 0.7004 (m-30) cc_final: 0.6791 (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: 1.4734 time to fit residues: 231.0922 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 : 0.836 ------------------------------------------------------------------------------- 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 75 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 chunk 23 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 259 HIS A 312 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.167334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137093 restraints weight = 7526.198| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.71 r_work: 0.3456 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7367 Z= 0.217 Angle : 0.517 6.417 10024 Z= 0.270 Chirality : 0.043 0.213 1123 Planarity : 0.004 0.049 1294 Dihedral : 5.683 71.193 976 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.93 % Allowed : 9.77 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 885 helix: 1.66 (0.27), residues: 385 sheet: 0.10 (0.45), residues: 133 loop : 0.14 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 177 HIS 0.003 0.001 HIS A 999 PHE 0.011 0.002 PHE A 773 TYR 0.012 0.002 TYR A 294 ARG 0.004 0.001 ARG A 820 *********************** 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 139 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.764 Fit side-chains REVERT: A 65 ARG cc_start: 0.6277 (ptt90) cc_final: 0.6071 (mtp180) REVERT: A 80 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: A 104 ARG cc_start: 0.7605 (ptt90) cc_final: 0.7325 (ptt90) REVERT: A 222 GLU cc_start: 0.6958 (pp20) cc_final: 0.6732 (tm-30) REVERT: A 280 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7891 (mtm110) REVERT: A 369 GLN cc_start: 0.7966 (mm110) cc_final: 0.7644 (mm110) REVERT: A 611 MET cc_start: 0.7985 (tpp) cc_final: 0.7706 (mmp) REVERT: A 827 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7662 (pmm-80) REVERT: A 970 ASP cc_start: 0.7382 (m-30) cc_final: 0.6924 (m-30) REVERT: A 996 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7133 (mptt) outliers start: 15 outliers final: 6 residues processed: 133 average time/residue: 1.1759 time to fit residues: 164.6456 Evaluate side-chains 122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125043 restraints weight = 7817.448| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.04 r_work: 0.3331 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7367 Z= 0.394 Angle : 0.613 8.488 10024 Z= 0.315 Chirality : 0.046 0.221 1123 Planarity : 0.005 0.047 1294 Dihedral : 6.201 77.451 976 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.47 % Allowed : 11.18 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.28), residues: 885 helix: 1.22 (0.26), residues: 390 sheet: 0.25 (0.43), residues: 121 loop : -0.25 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 177 HIS 0.005 0.001 HIS A 999 PHE 0.016 0.002 PHE A 978 TYR 0.015 0.002 TYR A 294 ARG 0.004 0.001 ARG A 181 *********************** 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: 27 poor density : 109 time to evaluate : 0.777 Fit side-chains REVERT: A 80 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: A 104 ARG cc_start: 0.7552 (ptt90) cc_final: 0.7248 (ptt90) REVERT: A 280 ARG cc_start: 0.7899 (mtm180) cc_final: 0.7658 (mtm110) REVERT: A 369 GLN cc_start: 0.7731 (mm110) cc_final: 0.7332 (mm110) REVERT: A 647 ASN cc_start: 0.7567 (t0) cc_final: 0.7278 (t0) REVERT: A 710 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: A 970 ASP cc_start: 0.7042 (m-30) cc_final: 0.6483 (m-30) REVERT: A 996 LYS cc_start: 0.7587 (mmtp) cc_final: 0.6963 (mptt) outliers start: 27 outliers final: 12 residues processed: 121 average time/residue: 1.3085 time to fit residues: 167.0057 Evaluate side-chains 117 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 602 THR 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 837 SER Chi-restraints excluded: chain A residue 1075 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 2 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.0870 chunk 47 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128506 restraints weight = 7870.555| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.07 r_work: 0.3365 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1581 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= 0.176 Angle : 0.493 5.650 10024 Z= 0.256 Chirality : 0.042 0.224 1123 Planarity : 0.004 0.042 1294 Dihedral : 6.041 77.065 976 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.96 % Allowed : 12.60 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 885 helix: 1.65 (0.27), residues: 385 sheet: -0.37 (0.43), residues: 133 loop : 0.08 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 177 HIS 0.003 0.001 HIS A 322 PHE 0.018 0.001 PHE A 898 TYR 0.013 0.001 TYR A 294 ARG 0.004 0.000 ARG A1059 *********************** 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 135 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.859 Fit side-chains REVERT: A 80 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: A 280 ARG cc_start: 0.7714 (mtm180) cc_final: 0.7474 (mtm110) REVERT: A 369 GLN cc_start: 0.7656 (mm110) cc_final: 0.7236 (mm110) REVERT: A 647 ASN cc_start: 0.7473 (t0) cc_final: 0.7188 (t0) REVERT: A 710 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: A 790 GLN cc_start: 0.6977 (tt0) cc_final: 0.6513 (mm-40) REVERT: A 827 ARG cc_start: 0.7933 (ptp-170) cc_final: 0.7483 (pmm-80) REVERT: A 970 ASP cc_start: 0.6902 (m-30) cc_final: 0.6358 (m-30) REVERT: A 996 LYS cc_start: 0.7500 (mmtp) cc_final: 0.6869 (mptt) REVERT: A 1048 ASP cc_start: 0.7312 (t70) cc_final: 0.7082 (t0) outliers start: 23 outliers final: 10 residues processed: 124 average time/residue: 1.2652 time to fit residues: 165.8118 Evaluate side-chains 119 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 130 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 413 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 85 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128429 restraints weight = 7722.805| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.05 r_work: 0.3359 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7367 Z= 0.198 Angle : 0.499 6.063 10024 Z= 0.258 Chirality : 0.042 0.245 1123 Planarity : 0.004 0.046 1294 Dihedral : 6.029 74.528 976 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.96 % Allowed : 12.98 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 885 helix: 1.76 (0.26), residues: 386 sheet: -0.42 (0.42), residues: 133 loop : 0.08 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 177 HIS 0.005 0.001 HIS A 999 PHE 0.020 0.002 PHE A 898 TYR 0.013 0.001 TYR A 294 ARG 0.005 0.000 ARG A 104 *********************** 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 132 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.821 Fit side-chains REVERT: A 65 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6704 (ttp-170) REVERT: A 80 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: A 104 ARG cc_start: 0.7429 (ptt90) cc_final: 0.7152 (ptt90) REVERT: A 280 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7562 (mtm110) REVERT: A 369 GLN cc_start: 0.7685 (mm110) cc_final: 0.7266 (mm110) REVERT: A 710 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: A 790 GLN cc_start: 0.7061 (tt0) cc_final: 0.6611 (mm-40) REVERT: A 805 ARG cc_start: 0.6720 (mmp-170) cc_final: 0.6071 (mmp-170) REVERT: A 819 ARG cc_start: 0.8474 (tpt170) cc_final: 0.8256 (tpt90) REVERT: A 827 ARG cc_start: 0.7976 (ptp-170) cc_final: 0.7516 (pmm-80) REVERT: A 970 ASP cc_start: 0.6904 (m-30) cc_final: 0.6374 (m-30) REVERT: A 996 LYS cc_start: 0.7503 (mmtp) cc_final: 0.6664 (mptt) REVERT: A 1048 ASP cc_start: 0.7439 (t70) cc_final: 0.7120 (t70) outliers start: 23 outliers final: 10 residues processed: 122 average time/residue: 1.3085 time to fit residues: 168.2020 Evaluate side-chains 116 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 93 ASP 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 642 VAL 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 837 SER 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 16 optimal weight: 0.0170 chunk 68 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 11 optimal weight: 0.0270 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 21 optimal weight: 0.0980 overall best weight: 0.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 166 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 = 0.3860 r_free = 0.3860 target = 0.165792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133977 restraints weight = 7757.420| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.02 r_work: 0.3418 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7367 Z= 0.131 Angle : 0.450 4.693 10024 Z= 0.235 Chirality : 0.041 0.240 1123 Planarity : 0.004 0.041 1294 Dihedral : 5.875 71.063 976 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.16 % Allowed : 15.55 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 885 helix: 2.21 (0.27), residues: 379 sheet: -0.51 (0.41), residues: 141 loop : 0.23 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 177 HIS 0.002 0.000 HIS A 322 PHE 0.015 0.001 PHE A 898 TYR 0.011 0.001 TYR A 294 ARG 0.004 0.000 ARG A 181 *********************** 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 120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.777 Fit side-chains REVERT: A 104 ARG cc_start: 0.7436 (ptt90) cc_final: 0.7152 (ptt90) REVERT: A 181 ARG cc_start: 0.7100 (ttt90) cc_final: 0.6862 (ttt90) REVERT: A 271 ASN cc_start: 0.7786 (m-40) cc_final: 0.7446 (m-40) REVERT: A 280 ARG cc_start: 0.7602 (mtm180) cc_final: 0.7386 (mtm110) REVERT: A 369 GLN cc_start: 0.7627 (mm110) cc_final: 0.7165 (mm110) REVERT: A 586 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 710 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: A 819 ARG cc_start: 0.8286 (tpt170) cc_final: 0.8046 (tpt90) REVERT: A 827 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7503 (pmm-80) REVERT: A 970 ASP cc_start: 0.6838 (m-30) cc_final: 0.6302 (m-30) REVERT: A 996 LYS cc_start: 0.7414 (mmtp) cc_final: 0.6543 (mptt) REVERT: A 1048 ASP cc_start: 0.7402 (t70) cc_final: 0.7060 (t70) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 1.3759 time to fit residues: 166.7483 Evaluate side-chains 109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 572 LEU 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 Chi-restraints excluded: chain A residue 1004 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126924 restraints weight = 7788.816| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.05 r_work: 0.3346 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7367 Z= 0.293 Angle : 0.546 7.332 10024 Z= 0.280 Chirality : 0.044 0.263 1123 Planarity : 0.004 0.049 1294 Dihedral : 6.180 73.774 976 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.70 % Allowed : 15.04 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.29), residues: 885 helix: 1.79 (0.26), residues: 385 sheet: 0.13 (0.43), residues: 125 loop : -0.07 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 177 HIS 0.005 0.001 HIS A 999 PHE 0.018 0.002 PHE A 898 TYR 0.014 0.002 TYR A 294 ARG 0.007 0.001 ARG A 325 *********************** 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 130 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.760 Fit side-chains REVERT: A 80 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: A 104 ARG cc_start: 0.7466 (ptt90) cc_final: 0.7226 (ptt90) REVERT: A 223 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 280 ARG cc_start: 0.7761 (mtm180) cc_final: 0.7545 (mtm110) REVERT: A 369 GLN cc_start: 0.7657 (mm110) cc_final: 0.7197 (mm110) REVERT: A 710 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: A 790 GLN cc_start: 0.7094 (tt0) cc_final: 0.6652 (mm-40) REVERT: A 805 ARG cc_start: 0.6705 (mmp-170) cc_final: 0.6387 (mmp-170) REVERT: A 819 ARG cc_start: 0.8520 (tpt170) cc_final: 0.8277 (tpt90) REVERT: A 827 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7607 (pmm-80) REVERT: A 970 ASP cc_start: 0.6837 (m-30) cc_final: 0.6269 (m-30) REVERT: A 996 LYS cc_start: 0.7545 (mmtp) cc_final: 0.6682 (mptt) REVERT: A 1048 ASP cc_start: 0.7429 (t70) cc_final: 0.7067 (t70) outliers start: 21 outliers final: 10 residues processed: 120 average time/residue: 1.3523 time to fit residues: 170.7353 Evaluate side-chains 120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 223 ILE 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 803 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 998 ASN Chi-restraints excluded: chain A residue 1004 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 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 = 0.3810 r_free = 0.3810 target = 0.161583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131438 restraints weight = 7887.350| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.70 r_work: 0.3390 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7367 Z= 0.346 Angle : 0.584 7.849 10024 Z= 0.299 Chirality : 0.045 0.298 1123 Planarity : 0.005 0.043 1294 Dihedral : 6.412 74.951 976 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.83 % Allowed : 15.55 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 885 helix: 1.43 (0.26), residues: 391 sheet: -0.04 (0.43), residues: 125 loop : -0.27 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 770 HIS 0.005 0.001 HIS A 999 PHE 0.023 0.002 PHE A 898 TYR 0.014 0.002 TYR A 294 ARG 0.006 0.001 ARG A 325 *********************** 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 131 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.797 Fit side-chains REVERT: A 80 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: A 181 ARG cc_start: 0.7461 (ttt90) cc_final: 0.7243 (ttt90) REVERT: A 369 GLN cc_start: 0.8028 (mm110) cc_final: 0.7702 (mm110) REVERT: A 710 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: A 819 ARG cc_start: 0.8634 (tpt170) cc_final: 0.8368 (tpt90) REVERT: A 827 ARG cc_start: 0.8166 (ptp-170) cc_final: 0.7891 (pmm-80) REVERT: A 970 ASP cc_start: 0.7394 (m-30) cc_final: 0.6872 (m-30) REVERT: A 996 LYS cc_start: 0.7842 (mmtp) cc_final: 0.7131 (mptt) REVERT: A 1048 ASP cc_start: 0.7587 (t70) cc_final: 0.7207 (t70) outliers start: 22 outliers final: 14 residues processed: 124 average time/residue: 1.3396 time to fit residues: 174.9518 Evaluate side-chains 120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 130 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 413 ILE 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 837 SER Chi-restraints excluded: chain A residue 994 VAL 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 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 56 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 790 GLN A1024 GLN A1052 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.161772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129565 restraints weight = 7818.218| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.04 r_work: 0.3378 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1875 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= 0.176 Angle : 0.489 5.422 10024 Z= 0.255 Chirality : 0.042 0.293 1123 Planarity : 0.004 0.043 1294 Dihedral : 6.242 73.421 976 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.80 % Allowed : 16.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 885 helix: 1.87 (0.26), residues: 384 sheet: -0.51 (0.42), residues: 143 loop : 0.12 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 177 HIS 0.003 0.001 HIS A 880 PHE 0.021 0.001 PHE A 898 TYR 0.013 0.001 TYR A 294 ARG 0.006 0.000 ARG A 104 *********************** 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: 14 poor density : 106 time to evaluate : 0.815 Fit side-chains REVERT: A 80 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: A 104 ARG cc_start: 0.7505 (ptt90) cc_final: 0.7227 (ptt90) REVERT: A 181 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6952 (ttt90) REVERT: A 369 GLN cc_start: 0.7694 (mm110) cc_final: 0.7248 (mm110) REVERT: A 710 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: A 819 ARG cc_start: 0.8476 (tpt170) cc_final: 0.8258 (tpt90) REVERT: A 827 ARG cc_start: 0.7987 (ptp-170) cc_final: 0.7620 (pmm-80) REVERT: A 970 ASP cc_start: 0.6784 (m-30) cc_final: 0.6254 (m-30) REVERT: A 996 LYS cc_start: 0.7638 (mmtp) cc_final: 0.6753 (mptt) REVERT: A 1048 ASP cc_start: 0.7276 (t70) cc_final: 0.6893 (t70) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 1.4464 time to fit residues: 171.5492 Evaluate side-chains 117 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU 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 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 790 GLN Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1004 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 271 ASN A 790 GLN A1024 GLN A1052 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128362 restraints weight = 7958.127| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.06 r_work: 0.3342 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7367 Z= 0.211 Angle : 0.506 5.998 10024 Z= 0.262 Chirality : 0.043 0.298 1123 Planarity : 0.004 0.044 1294 Dihedral : 6.262 72.444 976 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.93 % Allowed : 16.71 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 885 helix: 1.96 (0.26), residues: 378 sheet: -0.52 (0.42), residues: 143 loop : 0.12 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 177 HIS 0.003 0.001 HIS A 880 PHE 0.021 0.001 PHE A 898 TYR 0.013 0.001 TYR A 294 ARG 0.007 0.001 ARG A 325 ********************** 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 120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.803 Fit side-chains REVERT: A 80 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: A 104 ARG cc_start: 0.7519 (ptt90) cc_final: 0.7240 (ptt90) REVERT: A 181 ARG cc_start: 0.7172 (ttt90) cc_final: 0.6886 (ttt90) REVERT: A 369 GLN cc_start: 0.7656 (mm110) cc_final: 0.7177 (mm110) REVERT: A 710 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: A 819 ARG cc_start: 0.8461 (tpt170) cc_final: 0.8223 (tpt90) REVERT: A 823 GLU cc_start: 0.6779 (pp20) cc_final: 0.6559 (pp20) REVERT: A 827 ARG cc_start: 0.7985 (ptp-170) cc_final: 0.7612 (pmm-80) REVERT: A 970 ASP cc_start: 0.6731 (m-30) cc_final: 0.6169 (m-30) REVERT: A 996 LYS cc_start: 0.7575 (mmtp) cc_final: 0.6691 (mptt) REVERT: A 1048 ASP cc_start: 0.7259 (t70) cc_final: 0.6886 (t70) outliers start: 15 outliers final: 12 residues processed: 113 average time/residue: 1.4529 time to fit residues: 172.4184 Evaluate side-chains 119 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 413 ILE 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 790 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1004 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.0770 chunk 7 optimal weight: 0.4980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A1052 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.160213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127863 restraints weight = 7786.666| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.04 r_work: 0.3366 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7367 Z= 0.238 Angle : 0.522 6.333 10024 Z= 0.270 Chirality : 0.043 0.298 1123 Planarity : 0.004 0.044 1294 Dihedral : 6.294 72.014 976 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 16.84 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 885 helix: 1.71 (0.26), residues: 390 sheet: -0.12 (0.43), residues: 131 loop : -0.14 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 177 HIS 0.004 0.001 HIS A 880 PHE 0.021 0.002 PHE A 898 TYR 0.014 0.002 TYR A 294 ARG 0.007 0.001 ARG A 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5777.86 seconds wall clock time: 103 minutes 14.71 seconds (6194.71 seconds total)