Starting phenix.real_space_refine on Tue Feb 3 15:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9u_71423/02_2026/9p9u_71423.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9u_71423/02_2026/9p9u_71423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9u_71423/02_2026/9p9u_71423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9u_71423/02_2026/9p9u_71423.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9u_71423/02_2026/9p9u_71423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9u_71423/02_2026/9p9u_71423.map" } resolution = 3.27 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= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2854 2.51 5 N 745 2.21 5 O 778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4407 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4351 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 516} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'6JS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.93, per 1000 atoms: 0.21 Number of scatterers: 4407 At special positions: 0 Unit cell: (62.4, 105.664, 91.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 778 8.00 N 745 7.00 C 2854 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: 0.26 Conformation dependent library (CDL) restraints added in 235.0 milliseconds 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 42.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 734 through 745 removed outlier: 3.799A pdb=" N VAL A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'A' and resid 786 through 807 Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'A' and resid 858 through 863 Processing helix chain 'A' and resid 868 through 885 Processing helix chain 'A' and resid 895 through 897 No H-bonds generated for 'chain 'A' and resid 895 through 897' Processing helix chain 'A' and resid 898 through 906 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 936 through 949 Processing helix chain 'A' and resid 950 through 955 removed outlier: 3.888A pdb=" N TYR A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1096 removed outlier: 3.567A pdb=" N VAL A1096 " --> pdb=" O VAL A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1132 Processing helix chain 'A' and resid 1137 through 1158 Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1204 through 1208 Processing helix chain 'A' and resid 1209 through 1214 Processing helix chain 'A' and resid 1219 through 1236 Processing helix chain 'A' and resid 1248 through 1255 removed outlier: 4.411A pdb=" N SER A1252 " --> pdb=" O SER A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1277 removed outlier: 3.680A pdb=" N LYS A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS A1277 " --> pdb=" O ILE A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1299 Processing helix chain 'A' and resid 1301 through 1306 removed outlier: 3.902A pdb=" N TYR A1305 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1306 " --> pdb=" O PRO A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1301 through 1306' Processing sheet with id=AA1, first strand: chain 'A' and resid 688 through 696 removed outlier: 5.680A pdb=" N LYS A 690 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU A 706 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 702 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 701 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 722 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 819 through 823 removed outlier: 5.278A pdb=" N VAL A 821 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LYS A 828 " --> pdb=" O VAL A 821 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 823 " --> pdb=" O HIS A 826 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1032 through 1033 removed outlier: 6.192A pdb=" N ARG A1032 " --> pdb=" O ILE A1107 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N LEU A1104 " --> pdb=" O GLN A1118 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A1118 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A1053 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1160 through 1161 removed outlier: 3.510A pdb=" N VAL A1161 " --> pdb=" O LYS A1187 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1187 " --> pdb=" O VAL A1161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1170 through 1174 removed outlier: 3.687A pdb=" N LYS A1173 " --> pdb=" O HIS A1177 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N HIS A1177 " --> pdb=" O LYS A1173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1196 through 1197 178 hydrogen bonds defined for protein. 501 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1392 1.34 - 1.46: 1004 1.46 - 1.58: 2064 1.58 - 1.70: 1 1.70 - 1.81: 48 Bond restraints: 4509 Sorted by residual: bond pdb=" CB PRO A 890 " pdb=" CG PRO A 890 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.88e+00 bond pdb=" CG PRO A 890 " pdb=" CD PRO A 890 " ideal model delta sigma weight residual 1.503 1.566 -0.063 3.40e-02 8.65e+02 3.42e+00 bond pdb=" CB PRO A 709 " pdb=" CG PRO A 709 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.02e+00 bond pdb=" CB LYS A1256 " pdb=" CG LYS A1256 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CB PRO A1060 " pdb=" CG PRO A1060 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.54e+00 ... (remaining 4504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 5938 1.78 - 3.55: 126 3.55 - 5.33: 29 5.33 - 7.11: 7 7.11 - 8.89: 6 Bond angle restraints: 6106 Sorted by residual: angle pdb=" CA PRO A 890 " pdb=" N PRO A 890 " pdb=" CD PRO A 890 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" CA GLU A 710 " pdb=" CB GLU A 710 " pdb=" CG GLU A 710 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.83e+00 angle pdb=" CB MET A 884 " pdb=" CG MET A 884 " pdb=" SD MET A 884 " ideal model delta sigma weight residual 112.70 121.59 -8.89 3.00e+00 1.11e-01 8.78e+00 angle pdb=" CB LYS A1256 " pdb=" CG LYS A1256 " pdb=" CD LYS A1256 " ideal model delta sigma weight residual 111.30 118.06 -6.76 2.30e+00 1.89e-01 8.63e+00 angle pdb=" CB MET A1272 " pdb=" CG MET A1272 " pdb=" SD MET A1272 " ideal model delta sigma weight residual 112.70 121.11 -8.41 3.00e+00 1.11e-01 7.86e+00 ... (remaining 6101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 2328 16.06 - 32.12: 251 32.12 - 48.17: 106 48.17 - 64.23: 19 64.23 - 80.29: 3 Dihedral angle restraints: 2707 sinusoidal: 1120 harmonic: 1587 Sorted by residual: dihedral pdb=" CA LYS A 828 " pdb=" C LYS A 828 " pdb=" N ILE A 829 " pdb=" CA ILE A 829 " ideal model delta harmonic sigma weight residual 180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA VAL A 924 " pdb=" C VAL A 924 " pdb=" N LYS A 925 " pdb=" CA LYS A 925 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA MET A 921 " pdb=" C MET A 921 " pdb=" N ILE A 922 " pdb=" CA ILE A 922 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 415 0.034 - 0.069: 194 0.069 - 0.103: 40 0.103 - 0.137: 32 0.137 - 0.171: 4 Chirality restraints: 685 Sorted by residual: chirality pdb=" CG LEU A1306 " pdb=" CB LEU A1306 " pdb=" CD1 LEU A1306 " pdb=" CD2 LEU A1306 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA PRO A 890 " pdb=" N PRO A 890 " pdb=" C PRO A 890 " pdb=" CB PRO A 890 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA MET A1152 " pdb=" N MET A1152 " pdb=" C MET A1152 " pdb=" CB MET A1152 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 682 not shown) Planarity restraints: 755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 708 " 0.053 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO A 709 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 709 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 709 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1278 " 0.019 2.00e-02 2.50e+03 1.59e-02 6.34e+00 pdb=" CG TRP A1278 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A1278 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A1278 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1278 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1278 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1278 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1278 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1278 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1278 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 889 " 0.043 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO A 890 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 890 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 890 " 0.034 5.00e-02 4.00e+02 ... (remaining 752 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 49 2.62 - 3.19: 3831 3.19 - 3.76: 6870 3.76 - 4.33: 9372 4.33 - 4.90: 15062 Nonbonded interactions: 35184 Sorted by model distance: nonbonded pdb=" OD1 ASP A 918 " pdb=" OH TYR A1091 " model vdw 2.055 3.040 nonbonded pdb=" OH TYR A 789 " pdb=" OE1 GLN A 825 " model vdw 2.109 3.040 nonbonded pdb=" O LEU A1260 " pdb=" OH TYR A1271 " model vdw 2.141 3.040 nonbonded pdb=" O VAL A 924 " pdb=" N CYS A 926 " model vdw 2.167 3.120 nonbonded pdb=" O ALA A 858 " pdb=" OG SER A 861 " model vdw 2.235 3.040 ... (remaining 35179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 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 : 0.004 0.098 4509 Z= 0.149 Angle : 0.712 8.887 6106 Z= 0.362 Chirality : 0.045 0.171 685 Planarity : 0.006 0.079 755 Dihedral : 16.019 80.288 1681 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 0.63 % Allowed : 23.69 % Favored : 75.68 % 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: 0.52 (0.36), residues: 535 helix: 0.72 (0.36), residues: 205 sheet: 1.22 (0.80), residues: 42 loop : 0.04 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 938 TYR 0.022 0.002 TYR A 920 PHE 0.008 0.001 PHE A 886 TRP 0.043 0.002 TRP A1278 HIS 0.002 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4509) covalent geometry : angle 0.71214 ( 6106) hydrogen bonds : bond 0.18973 ( 178) hydrogen bonds : angle 6.15297 ( 501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 715 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8016 (tttm) REVERT: A 938 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7964 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.0837 time to fit residues: 12.8590 Evaluate side-chains 123 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 GLN A1221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.169700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.155510 restraints weight = 7235.624| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 3.37 r_work: 0.3963 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4509 Z= 0.141 Angle : 0.630 6.341 6106 Z= 0.317 Chirality : 0.045 0.152 685 Planarity : 0.006 0.068 755 Dihedral : 5.520 56.976 598 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.67 % Favored : 95.14 % Rotamer: Outliers : 3.14 % Allowed : 20.75 % Favored : 76.10 % 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: 0.58 (0.36), residues: 535 helix: 0.77 (0.37), residues: 208 sheet: 1.30 (0.81), residues: 41 loop : 0.07 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 938 TYR 0.015 0.002 TYR A 920 PHE 0.004 0.001 PHE A 832 TRP 0.023 0.002 TRP A1278 HIS 0.003 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4509) covalent geometry : angle 0.62977 ( 6106) hydrogen bonds : bond 0.04807 ( 178) hydrogen bonds : angle 4.96933 ( 501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 952 GLN cc_start: 0.7103 (mp-120) cc_final: 0.6758 (mp-120) REVERT: A 1221 GLN cc_start: 0.8155 (mm110) cc_final: 0.7881 (mp10) outliers start: 15 outliers final: 8 residues processed: 128 average time/residue: 0.0515 time to fit residues: 8.2210 Evaluate side-chains 118 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1212 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.171254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.157432 restraints weight = 7198.506| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 3.29 r_work: 0.3970 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4509 Z= 0.122 Angle : 0.595 6.854 6106 Z= 0.296 Chirality : 0.045 0.156 685 Planarity : 0.005 0.055 755 Dihedral : 4.898 39.163 594 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.49 % Favored : 95.33 % Rotamer: Outliers : 3.56 % Allowed : 22.22 % Favored : 74.21 % 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: 0.62 (0.36), residues: 535 helix: 0.85 (0.37), residues: 208 sheet: 1.15 (0.91), residues: 36 loop : 0.09 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 938 TYR 0.014 0.001 TYR A 920 PHE 0.004 0.001 PHE A 832 TRP 0.020 0.002 TRP A1278 HIS 0.003 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4509) covalent geometry : angle 0.59460 ( 6106) hydrogen bonds : bond 0.04082 ( 178) hydrogen bonds : angle 4.71929 ( 501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 828 LYS cc_start: 0.8052 (ptmt) cc_final: 0.7796 (ptmm) REVERT: A 852 VAL cc_start: 0.6060 (OUTLIER) cc_final: 0.5688 (m) REVERT: A 882 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 952 GLN cc_start: 0.7054 (mp-120) cc_final: 0.6753 (mp-120) REVERT: A 1187 LYS cc_start: 0.8388 (mmtm) cc_final: 0.7766 (mmtm) outliers start: 17 outliers final: 10 residues processed: 125 average time/residue: 0.0623 time to fit residues: 9.7483 Evaluate side-chains 123 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1235 MET Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.169680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.155673 restraints weight = 7201.487| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.33 r_work: 0.3963 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4509 Z= 0.134 Angle : 0.599 10.042 6106 Z= 0.297 Chirality : 0.045 0.190 685 Planarity : 0.005 0.048 755 Dihedral : 4.827 36.033 594 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 3.98 % Allowed : 20.75 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.55 (0.37), residues: 535 helix: 0.87 (0.37), residues: 208 sheet: 0.95 (0.91), residues: 37 loop : 0.01 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 938 TYR 0.020 0.002 TYR A 803 PHE 0.005 0.001 PHE A1039 TRP 0.027 0.002 TRP A1278 HIS 0.003 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4509) covalent geometry : angle 0.59893 ( 6106) hydrogen bonds : bond 0.03809 ( 178) hydrogen bonds : angle 4.69083 ( 501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 801 MET cc_start: 0.6895 (mmm) cc_final: 0.6570 (mmm) REVERT: A 831 ASP cc_start: 0.7216 (t0) cc_final: 0.6998 (t0) REVERT: A 852 VAL cc_start: 0.6149 (OUTLIER) cc_final: 0.5761 (m) REVERT: A 882 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 920 TYR cc_start: 0.8074 (t80) cc_final: 0.7848 (t80) REVERT: A 952 GLN cc_start: 0.7093 (mp-120) cc_final: 0.6779 (mp-120) REVERT: A 1187 LYS cc_start: 0.8411 (mmtm) cc_final: 0.7776 (mmtm) outliers start: 19 outliers final: 9 residues processed: 127 average time/residue: 0.0803 time to fit residues: 12.4962 Evaluate side-chains 125 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1274 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 chunk 12 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.170944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.156910 restraints weight = 7240.358| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.35 r_work: 0.3943 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4509 Z= 0.113 Angle : 0.571 11.283 6106 Z= 0.281 Chirality : 0.044 0.150 685 Planarity : 0.005 0.044 755 Dihedral : 4.726 37.143 594 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.49 % Favored : 95.33 % Rotamer: Outliers : 2.94 % Allowed : 22.22 % Favored : 74.84 % 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: 0.72 (0.37), residues: 535 helix: 0.98 (0.38), residues: 208 sheet: 0.98 (0.89), residues: 37 loop : 0.15 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 938 TYR 0.016 0.001 TYR A 803 PHE 0.003 0.001 PHE A1039 TRP 0.029 0.002 TRP A1278 HIS 0.003 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4509) covalent geometry : angle 0.57071 ( 6106) hydrogen bonds : bond 0.03499 ( 178) hydrogen bonds : angle 4.63628 ( 501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 MET cc_start: 0.6879 (mmm) cc_final: 0.6630 (mmm) REVERT: A 831 ASP cc_start: 0.7294 (t0) cc_final: 0.6904 (t0) REVERT: A 882 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 952 GLN cc_start: 0.6991 (mp10) cc_final: 0.6627 (mp10) REVERT: A 1072 LYS cc_start: 0.7154 (tttt) cc_final: 0.6720 (pttt) REVERT: A 1232 TRP cc_start: 0.8310 (t60) cc_final: 0.7902 (t60) outliers start: 14 outliers final: 12 residues processed: 128 average time/residue: 0.0852 time to fit residues: 13.3971 Evaluate side-chains 127 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1275 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 870 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.167747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.153203 restraints weight = 7393.792| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 3.50 r_work: 0.3917 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4509 Z= 0.156 Angle : 0.600 11.918 6106 Z= 0.301 Chirality : 0.045 0.147 685 Planarity : 0.005 0.042 755 Dihedral : 4.839 33.703 594 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.67 % Favored : 94.95 % Rotamer: Outliers : 4.40 % Allowed : 21.59 % Favored : 74.00 % 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: 0.60 (0.37), residues: 535 helix: 0.96 (0.38), residues: 208 sheet: 1.08 (0.89), residues: 37 loop : -0.01 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 938 TYR 0.013 0.002 TYR A 803 PHE 0.006 0.001 PHE A1183 TRP 0.033 0.002 TRP A1278 HIS 0.003 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4509) covalent geometry : angle 0.60001 ( 6106) hydrogen bonds : bond 0.03741 ( 178) hydrogen bonds : angle 4.75239 ( 501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 ASP cc_start: 0.7296 (t0) cc_final: 0.6847 (t0) REVERT: A 882 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 952 GLN cc_start: 0.7120 (mp10) cc_final: 0.6748 (mp10) REVERT: A 1072 LYS cc_start: 0.7292 (tttt) cc_final: 0.7083 (tttt) REVERT: A 1168 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7577 (mtm110) outliers start: 21 outliers final: 17 residues processed: 128 average time/residue: 0.0847 time to fit residues: 13.2579 Evaluate side-chains 133 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 947 MET Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1275 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 50 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.168245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.154097 restraints weight = 7215.446| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 3.36 r_work: 0.3923 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4509 Z= 0.142 Angle : 0.597 11.786 6106 Z= 0.294 Chirality : 0.044 0.156 685 Planarity : 0.005 0.042 755 Dihedral : 4.782 32.664 594 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.67 % Favored : 94.95 % Rotamer: Outliers : 3.77 % Allowed : 21.80 % Favored : 74.42 % 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: 0.60 (0.37), residues: 535 helix: 0.90 (0.37), residues: 208 sheet: 1.13 (0.89), residues: 37 loop : 0.03 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 908 TYR 0.013 0.002 TYR A 803 PHE 0.005 0.001 PHE A1183 TRP 0.029 0.002 TRP A 856 HIS 0.003 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4509) covalent geometry : angle 0.59684 ( 6106) hydrogen bonds : bond 0.03615 ( 178) hydrogen bonds : angle 4.76359 ( 501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 ASP cc_start: 0.7310 (t0) cc_final: 0.6811 (t0) REVERT: A 882 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 952 GLN cc_start: 0.7099 (mp10) cc_final: 0.6771 (mp10) REVERT: A 1072 LYS cc_start: 0.7372 (tttt) cc_final: 0.7018 (tttt) REVERT: A 1168 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7548 (mtm110) REVERT: A 1179 LYS cc_start: 0.7295 (mttt) cc_final: 0.7002 (tttt) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.0827 time to fit residues: 12.9037 Evaluate side-chains 131 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 947 MET Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.167988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.153618 restraints weight = 7281.369| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 3.45 r_work: 0.3935 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4509 Z= 0.148 Angle : 0.615 11.714 6106 Z= 0.304 Chirality : 0.044 0.153 685 Planarity : 0.005 0.041 755 Dihedral : 4.869 32.710 594 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.86 % Favored : 94.77 % Rotamer: Outliers : 4.19 % Allowed : 22.22 % Favored : 73.58 % 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: 0.50 (0.36), residues: 535 helix: 0.86 (0.37), residues: 208 sheet: 1.16 (0.90), residues: 37 loop : -0.08 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 938 TYR 0.013 0.002 TYR A 803 PHE 0.005 0.001 PHE A1183 TRP 0.032 0.002 TRP A1278 HIS 0.003 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4509) covalent geometry : angle 0.61491 ( 6106) hydrogen bonds : bond 0.03642 ( 178) hydrogen bonds : angle 4.77604 ( 501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 MET cc_start: 0.6944 (mmm) cc_final: 0.6712 (mmm) REVERT: A 831 ASP cc_start: 0.7313 (t0) cc_final: 0.6774 (t0) REVERT: A 882 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 899 ILE cc_start: 0.8021 (mt) cc_final: 0.7774 (mm) REVERT: A 952 GLN cc_start: 0.7120 (mp10) cc_final: 0.6780 (mp10) REVERT: A 1072 LYS cc_start: 0.7408 (tttt) cc_final: 0.7145 (tttt) REVERT: A 1168 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7599 (mtm110) REVERT: A 1179 LYS cc_start: 0.7324 (mttt) cc_final: 0.6985 (tttt) REVERT: A 1187 LYS cc_start: 0.8407 (mmtm) cc_final: 0.7714 (mmtm) outliers start: 20 outliers final: 18 residues processed: 129 average time/residue: 0.0698 time to fit residues: 10.9641 Evaluate side-chains 136 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 947 MET Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1084 LYS Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1288 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.167676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.153307 restraints weight = 7169.893| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.39 r_work: 0.3905 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4509 Z= 0.184 Angle : 0.652 11.097 6106 Z= 0.321 Chirality : 0.046 0.196 685 Planarity : 0.005 0.040 755 Dihedral : 4.994 35.675 594 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.05 % Favored : 94.58 % Rotamer: Outliers : 4.40 % Allowed : 22.43 % Favored : 73.17 % 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: 0.39 (0.36), residues: 535 helix: 0.74 (0.37), residues: 208 sheet: 1.11 (0.88), residues: 37 loop : -0.12 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 938 TYR 0.016 0.002 TYR A1271 PHE 0.007 0.001 PHE A1183 TRP 0.046 0.002 TRP A1278 HIS 0.004 0.001 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4509) covalent geometry : angle 0.65211 ( 6106) hydrogen bonds : bond 0.03929 ( 178) hydrogen bonds : angle 4.88362 ( 501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 CYS cc_start: 0.4569 (OUTLIER) cc_final: 0.4291 (m) REVERT: A 817 ARG cc_start: 0.8203 (ptt-90) cc_final: 0.7861 (ptt-90) REVERT: A 831 ASP cc_start: 0.7338 (t0) cc_final: 0.6769 (t0) REVERT: A 882 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 952 GLN cc_start: 0.7130 (mp10) cc_final: 0.6580 (mp10) REVERT: A 1072 LYS cc_start: 0.7472 (tttt) cc_final: 0.7162 (tttt) REVERT: A 1168 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7578 (mtm110) REVERT: A 1179 LYS cc_start: 0.7346 (mttt) cc_final: 0.7021 (tttt) outliers start: 21 outliers final: 15 residues processed: 129 average time/residue: 0.0670 time to fit residues: 10.4989 Evaluate side-chains 131 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 947 MET Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1288 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.167044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.152546 restraints weight = 7154.559| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.41 r_work: 0.3918 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4509 Z= 0.168 Angle : 0.655 10.490 6106 Z= 0.324 Chirality : 0.046 0.182 685 Planarity : 0.005 0.041 755 Dihedral : 5.014 34.497 594 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.67 % Favored : 94.95 % Rotamer: Outliers : 3.14 % Allowed : 23.06 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.36), residues: 535 helix: 0.68 (0.37), residues: 208 sheet: 1.17 (0.89), residues: 37 loop : -0.18 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 938 TYR 0.017 0.002 TYR A1271 PHE 0.006 0.001 PHE A1183 TRP 0.042 0.002 TRP A1278 HIS 0.005 0.001 HIS A1100 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4509) covalent geometry : angle 0.65461 ( 6106) hydrogen bonds : bond 0.03829 ( 178) hydrogen bonds : angle 4.89434 ( 501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 ASP cc_start: 0.7335 (t0) cc_final: 0.6767 (t0) REVERT: A 882 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 952 GLN cc_start: 0.7139 (mp10) cc_final: 0.6589 (mp10) REVERT: A 1072 LYS cc_start: 0.7502 (tttt) cc_final: 0.7181 (tttt) REVERT: A 1093 MET cc_start: 0.8477 (ttm) cc_final: 0.8178 (ttm) REVERT: A 1168 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7573 (mtm110) REVERT: A 1179 LYS cc_start: 0.7282 (mttt) cc_final: 0.6957 (tttt) outliers start: 15 outliers final: 15 residues processed: 125 average time/residue: 0.0531 time to fit residues: 8.2295 Evaluate side-chains 130 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 947 MET Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1288 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.0010 chunk 52 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.168984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.154595 restraints weight = 7304.800| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.44 r_work: 0.3941 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4509 Z= 0.129 Angle : 0.625 10.081 6106 Z= 0.307 Chirality : 0.045 0.167 685 Planarity : 0.005 0.043 755 Dihedral : 4.868 37.567 594 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.93 % Favored : 95.70 % Rotamer: Outliers : 3.35 % Allowed : 23.27 % Favored : 73.38 % 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: 0.42 (0.37), residues: 535 helix: 0.80 (0.37), residues: 208 sheet: 1.06 (0.90), residues: 37 loop : -0.13 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 938 TYR 0.017 0.002 TYR A1271 PHE 0.004 0.001 PHE A1183 TRP 0.037 0.002 TRP A1278 HIS 0.005 0.001 HIS A1177 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4509) covalent geometry : angle 0.62506 ( 6106) hydrogen bonds : bond 0.03584 ( 178) hydrogen bonds : angle 4.80101 ( 501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1022.27 seconds wall clock time: 18 minutes 15.69 seconds (1095.69 seconds total)