Starting phenix.real_space_refine on Fri Sep 11 08:32:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w64_21552/09_2026/6w64_21552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w64_21552/09_2026/6w64_21552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w64_21552/09_2026/6w64_21552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w64_21552/09_2026/6w64_21552.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6w64_21552/09_2026/6w64_21552.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w64_21552/09_2026/6w64_21552.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w64_21552/09_2026/6w64_21552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w64_21552/09_2026/6w64_21552.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 56 5.49 5 S 34 5.16 5 C 5213 2.51 5 N 1474 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8505 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7331 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 32, 'TRANS': 895} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 4, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 805 Classifications: {'RNAv2': 38} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 13, 'rna3p_pyr': 14} Link IDs: {'rna2p': 11, 'rna3p': 26} Chain: "C" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 1.80, per 1000 atoms: 0.21 Number of scatterers: 8505 At special positions: 0 Unit cell: (85.05, 128.1, 108.15, 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 34 16.00 P 56 15.00 O 1728 8.00 N 1474 7.00 C 5213 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: 0.89 Conformation dependent library (CDL) restraints added in 267.9 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 55.7% alpha, 7.2% beta 13 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.630A pdb=" N LEU A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 297 through 332 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 371 through 393 removed outlier: 4.539A pdb=" N THR A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 422 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 708 through 721 removed outlier: 3.804A pdb=" N LYS A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.531A pdb=" N ILE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 771 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.569A pdb=" N ALA A 775 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 787 Processing helix chain 'A' and resid 800 through 822 Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 846 through 886 Processing helix chain 'A' and resid 905 through 914 removed outlier: 3.638A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 967 through 971 Processing helix chain 'A' and resid 972 through 984 Processing helix chain 'A' and resid 990 through 1008 Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1018 through 1033 Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1090 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 7.423A pdb=" N ASN A 477 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY A 486 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 479 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE A 488 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU A 485 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 523 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 530 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.595A pdb=" N LYS A 81 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 683 removed outlier: 6.268A pdb=" N GLU A 660 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 680 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 669 through 670 Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 689 Processing sheet with id=AA6, first strand: chain 'A' and resid 893 through 894 removed outlier: 7.012A pdb=" N GLY A 893 " --> pdb=" O VAL A 939 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1050 406 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1268 1.28 - 1.41: 2320 1.41 - 1.54: 5026 1.54 - 1.68: 118 1.68 - 1.81: 58 Bond restraints: 8790 Sorted by residual: bond pdb=" C PHE A 80 " pdb=" O PHE A 80 " ideal model delta sigma weight residual 1.233 1.148 0.084 1.12e-02 7.97e+03 5.68e+01 bond pdb=" N ARG A 962 " pdb=" CA ARG A 962 " ideal model delta sigma weight residual 1.454 1.493 -0.038 1.17e-02 7.31e+03 1.07e+01 bond pdb=" N LYS A 81 " pdb=" CA LYS A 81 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.23e-02 6.61e+03 1.03e+01 bond pdb=" C ASN A1064 " pdb=" N GLY A1065 " ideal model delta sigma weight residual 1.331 1.376 -0.046 1.46e-02 4.69e+03 9.74e+00 bond pdb=" N GLY A 682 " pdb=" CA GLY A 682 " ideal model delta sigma weight residual 1.448 1.480 -0.031 1.00e-02 1.00e+04 9.62e+00 ... (remaining 8785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 11723 1.75 - 3.50: 314 3.50 - 5.25: 67 5.25 - 6.99: 2 6.99 - 8.74: 3 Bond angle restraints: 12109 Sorted by residual: angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 103.36 110.25 -6.89 8.80e-01 1.29e+00 6.14e+01 angle pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" O PHE A 80 " ideal model delta sigma weight residual 120.89 112.15 8.74 1.27e+00 6.20e-01 4.74e+01 angle pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N LYS A 81 " ideal model delta sigma weight residual 115.75 123.12 -7.37 1.08e+00 8.57e-01 4.66e+01 angle pdb=" C ASN A1064 " pdb=" N GLY A1065 " pdb=" CA GLY A1065 " ideal model delta sigma weight residual 121.41 129.72 -8.31 1.96e+00 2.60e-01 1.80e+01 angle pdb=" N3 DT C 17 " pdb=" C4 DT C 17 " pdb=" O4 DT C 17 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.62e+01 ... (remaining 12104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.65: 4991 29.65 - 59.31: 197 59.31 - 88.96: 29 88.96 - 118.62: 0 118.62 - 148.27: 1 Dihedral angle restraints: 5218 sinusoidal: 2485 harmonic: 2733 Sorted by residual: dihedral pdb=" C4' C B -8 " pdb=" C3' C B -8 " pdb=" C2' C B -8 " pdb=" C1' C B -8 " ideal model delta sinusoidal sigma weight residual 36.34 -37.12 73.47 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' C B -11 " pdb=" C3' C B -11 " pdb=" C2' C B -11 " pdb=" C1' C B -11 " ideal model delta sinusoidal sigma weight residual 36.34 -36.86 73.20 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" C1' G B 1 " ideal model delta sinusoidal sigma weight residual 36.34 -36.76 73.10 1 3.10e+00 1.04e-01 7.09e+02 ... (remaining 5215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1141 0.058 - 0.117: 136 0.117 - 0.175: 29 0.175 - 0.234: 38 0.234 - 0.292: 23 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C2' C B -22 " pdb=" C3' C B -22 " pdb=" O2' C B -22 " pdb=" C1' C B -22 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' G B 1 " pdb=" C3' G B 1 " pdb=" O2' G B 1 " pdb=" C1' G B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' U B -17 " pdb=" C3' U B -17 " pdb=" O2' U B -17 " pdb=" C1' U B -17 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1364 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 681 " -0.017 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C SER A 681 " 0.055 2.00e-02 2.50e+03 pdb=" O SER A 681 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY A 682 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 80 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C PHE A 80 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE A 80 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 81 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 96 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ASN A 96 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN A 96 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 97 " -0.011 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 830 2.74 - 3.28: 8889 3.28 - 3.82: 14483 3.82 - 4.36: 16738 4.36 - 4.90: 28352 Nonbonded interactions: 69292 Sorted by model distance: nonbonded pdb=" NH2 ARG A 57 " pdb=" OD1 ASP A 72 " model vdw 2.196 3.120 nonbonded pdb=" O SER A 981 " pdb=" OG SER A 984 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG A 853 " pdb=" OE2 GLU A 857 " model vdw 2.206 3.120 nonbonded pdb=" O ASN A 96 " pdb=" ND2 ASN A 96 " model vdw 2.207 3.120 nonbonded pdb=" O TYR A 104 " pdb=" OG SER A 105 " model vdw 2.216 3.040 ... (remaining 69287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8790 Z= 0.244 Angle : 0.677 8.742 12109 Z= 0.414 Chirality : 0.063 0.292 1367 Planarity : 0.003 0.032 1338 Dihedral : 15.259 148.269 3450 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.99 % Favored : 92.90 % Rotamer: Outliers : 1.29 % Allowed : 3.10 % Favored : 95.60 % 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: 0.30 (0.29), residues: 916 helix: 2.21 (0.24), residues: 501 sheet: -2.20 (0.54), residues: 74 loop : -2.47 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 918 TYR 0.024 0.001 TYR A 695 PHE 0.007 0.001 PHE A 911 TRP 0.010 0.001 TRP A 79 HIS 0.004 0.001 HIS A 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.24 ( 8790) covalent geometry : angle 0.67693 / 0.41 (12109) hydrogen bonds : bond 0.15680 / 10.44 ( 439) hydrogen bonds : angle 5.75751 / 4.15 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 248 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PRO cc_start: 0.8928 (Cg_endo) cc_final: 0.8659 (Cg_exo) REVERT: A 539 GLU cc_start: 0.4957 (tp30) cc_final: 0.3806 (tp30) REVERT: A 806 MET cc_start: 0.7081 (ttp) cc_final: 0.6737 (ptp) REVERT: A 850 PHE cc_start: 0.8922 (t80) cc_final: 0.8486 (t80) REVERT: A 918 ARG cc_start: 0.6123 (mmm-85) cc_final: 0.5806 (mmm-85) REVERT: A 929 MET cc_start: 0.7474 (mtt) cc_final: 0.7214 (mtp) REVERT: A 940 ASN cc_start: 0.7558 (t0) cc_final: 0.6847 (p0) REVERT: A 1074 ASP cc_start: 0.6321 (p0) cc_final: 0.5871 (p0) outliers start: 10 outliers final: 4 residues processed: 256 average time/residue: 0.1073 time to fit residues: 36.7460 Evaluate side-chains 145 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 890 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS A 471 GLN ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.145833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.119740 restraints weight = 18601.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.120592 restraints weight = 14878.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121615 restraints weight = 13041.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.122282 restraints weight = 9790.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124009 restraints weight = 9371.517| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 8790 Z= 0.273 Angle : 1.189 21.086 12109 Z= 0.517 Chirality : 0.101 1.257 1367 Planarity : 0.005 0.045 1338 Dihedral : 17.005 140.270 1666 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.85 % Allowed : 12.16 % Favored : 84.99 % 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: -0.34 (0.28), residues: 916 helix: 1.52 (0.23), residues: 512 sheet: -2.47 (0.54), residues: 73 loop : -2.60 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 779 TYR 0.025 0.002 TYR A 406 PHE 0.022 0.002 PHE A 743 TRP 0.023 0.003 TRP A 915 HIS 0.005 0.001 HIS A 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.27 ( 8790) covalent geometry : angle 1.18859 / 0.52 (12109) hydrogen bonds : bond 0.05781 / 3.46 ( 439) hydrogen bonds : angle 4.99324 / 3.59 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.5898 (tpt) cc_final: 0.5415 (tpt) REVERT: A 37 LEU cc_start: 0.8318 (mt) cc_final: 0.7898 (mt) REVERT: A 159 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6987 (tp30) REVERT: A 165 SER cc_start: 0.5435 (p) cc_final: 0.5110 (p) REVERT: A 460 LYS cc_start: 0.8547 (tttm) cc_final: 0.8323 (ttmt) REVERT: A 806 MET cc_start: 0.7779 (ttp) cc_final: 0.7302 (ttp) REVERT: A 940 ASN cc_start: 0.7721 (t0) cc_final: 0.7087 (p0) REVERT: A 959 PHE cc_start: 0.7710 (m-10) cc_final: 0.7437 (m-80) outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 0.0938 time to fit residues: 20.8753 Evaluate side-chains 137 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.144566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.119251 restraints weight = 18720.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.120734 restraints weight = 14430.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121949 restraints weight = 11396.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121722 restraints weight = 9405.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121986 restraints weight = 8881.307| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8790 Z= 0.236 Angle : 0.982 20.435 12109 Z= 0.442 Chirality : 0.075 0.707 1367 Planarity : 0.004 0.044 1338 Dihedral : 17.502 154.011 1661 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.72 % Allowed : 14.88 % Favored : 82.41 % 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: -0.43 (0.28), residues: 916 helix: 1.55 (0.23), residues: 498 sheet: -2.45 (0.54), residues: 73 loop : -2.67 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 22 TYR 0.025 0.003 TYR A 996 PHE 0.030 0.002 PHE A 80 TRP 0.028 0.003 TRP A 915 HIS 0.011 0.002 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 ( 8790) covalent geometry : angle 0.98231 / 0.44 (12109) hydrogen bonds : bond 0.05338 / 3.22 ( 439) hydrogen bonds : angle 4.85185 / 3.49 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6161 (tpt) cc_final: 0.5739 (tpt) REVERT: A 159 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7023 (tp30) REVERT: A 460 LYS cc_start: 0.8616 (tttm) cc_final: 0.8401 (ttmt) REVERT: A 595 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7502 (pp) REVERT: A 641 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7636 (ttmm) REVERT: A 767 SER cc_start: 0.8227 (m) cc_final: 0.8009 (t) REVERT: A 940 ASN cc_start: 0.7857 (t0) cc_final: 0.7210 (p0) outliers start: 21 outliers final: 17 residues processed: 145 average time/residue: 0.0841 time to fit residues: 17.6837 Evaluate side-chains 133 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 711 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.146976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.120921 restraints weight = 18881.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.120411 restraints weight = 14099.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.121185 restraints weight = 12586.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121787 restraints weight = 10786.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.122257 restraints weight = 9591.368| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8790 Z= 0.176 Angle : 0.877 18.380 12109 Z= 0.401 Chirality : 0.064 0.517 1367 Planarity : 0.004 0.032 1338 Dihedral : 17.442 150.438 1661 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.49 % Allowed : 15.65 % Favored : 80.85 % 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: -0.29 (0.28), residues: 916 helix: 1.72 (0.23), residues: 498 sheet: -2.67 (0.49), residues: 85 loop : -2.60 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 769 TYR 0.025 0.002 TYR A 963 PHE 0.028 0.002 PHE A 80 TRP 0.011 0.002 TRP A 48 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 8790) covalent geometry : angle 0.87730 / 0.40 (12109) hydrogen bonds : bond 0.04781 / 2.87 ( 439) hydrogen bonds : angle 4.59984 / 3.33 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.6238 (tpt) cc_final: 0.5814 (tpt) REVERT: A 86 ASN cc_start: 0.8474 (p0) cc_final: 0.8212 (p0) REVERT: A 116 TYR cc_start: 0.8385 (t80) cc_final: 0.8179 (t80) REVERT: A 159 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6901 (tp30) REVERT: A 176 MET cc_start: 0.6439 (ppp) cc_final: 0.6024 (tmm) REVERT: A 460 LYS cc_start: 0.8556 (tttm) cc_final: 0.8338 (ttmt) REVERT: A 940 ASN cc_start: 0.7916 (t0) cc_final: 0.7299 (p0) outliers start: 27 outliers final: 17 residues processed: 144 average time/residue: 0.0751 time to fit residues: 16.1219 Evaluate side-chains 138 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 9.9990 chunk 76 optimal weight: 0.0970 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN A 384 HIS A 616 ASN A 770 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.141000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.114877 restraints weight = 18993.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115335 restraints weight = 15370.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.116445 restraints weight = 13910.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.116543 restraints weight = 10383.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117082 restraints weight = 9867.756| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8790 Z= 0.284 Angle : 0.961 18.572 12109 Z= 0.450 Chirality : 0.066 0.473 1367 Planarity : 0.005 0.039 1338 Dihedral : 17.649 152.507 1661 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 3.75 % Allowed : 16.43 % Favored : 79.82 % 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 (0.28), residues: 916 helix: 1.39 (0.23), residues: 501 sheet: -2.52 (0.54), residues: 83 loop : -2.68 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 769 TYR 0.027 0.003 TYR A 963 PHE 0.023 0.003 PHE A 476 TRP 0.024 0.003 TRP A 511 HIS 0.009 0.002 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.28 ( 8790) covalent geometry : angle 0.96065 / 0.45 (12109) hydrogen bonds : bond 0.05427 / 3.36 ( 439) hydrogen bonds : angle 4.98975 / 3.62 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6417 (tpt) cc_final: 0.6002 (tpt) REVERT: A 34 MET cc_start: 0.8188 (mmm) cc_final: 0.7896 (mmm) REVERT: A 159 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6804 (tp30) REVERT: A 176 MET cc_start: 0.6425 (ppp) cc_final: 0.6025 (tmm) REVERT: A 539 GLU cc_start: 0.4551 (tp30) cc_final: 0.3252 (tp30) REVERT: A 940 ASN cc_start: 0.8113 (t0) cc_final: 0.7503 (p0) REVERT: A 948 ASP cc_start: 0.7574 (t0) cc_final: 0.7290 (t0) REVERT: A 1043 ARG cc_start: 0.6179 (mpt180) cc_final: 0.5134 (tpp80) outliers start: 29 outliers final: 26 residues processed: 134 average time/residue: 0.0893 time to fit residues: 16.9598 Evaluate side-chains 134 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 82 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.145797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120235 restraints weight = 18541.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121690 restraints weight = 14858.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.122672 restraints weight = 11411.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122905 restraints weight = 9130.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.123057 restraints weight = 8921.547| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8790 Z= 0.165 Angle : 0.841 16.371 12109 Z= 0.392 Chirality : 0.060 0.495 1367 Planarity : 0.004 0.042 1338 Dihedral : 17.591 157.211 1661 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.10 % Allowed : 18.76 % Favored : 78.14 % 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: -0.38 (0.28), residues: 916 helix: 1.64 (0.23), residues: 499 sheet: -2.66 (0.49), residues: 86 loop : -2.66 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 769 TYR 0.019 0.002 TYR A 406 PHE 0.022 0.002 PHE A 743 TRP 0.024 0.002 TRP A 915 HIS 0.009 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 ( 8790) covalent geometry : angle 0.84149 / 0.39 (12109) hydrogen bonds : bond 0.04614 / 2.85 ( 439) hydrogen bonds : angle 4.67174 / 3.40 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6086 (tpt) cc_final: 0.5628 (tpt) REVERT: A 37 LEU cc_start: 0.8219 (mt) cc_final: 0.7830 (mt) REVERT: A 116 TYR cc_start: 0.8416 (t80) cc_final: 0.8189 (t80) REVERT: A 159 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6753 (tp30) REVERT: A 176 MET cc_start: 0.6370 (ppp) cc_final: 0.5943 (tmm) REVERT: A 940 ASN cc_start: 0.7966 (t0) cc_final: 0.7379 (p0) REVERT: A 948 ASP cc_start: 0.7314 (t0) cc_final: 0.7048 (t0) REVERT: A 1043 ARG cc_start: 0.5864 (mpt180) cc_final: 0.4926 (tpp80) outliers start: 24 outliers final: 20 residues processed: 139 average time/residue: 0.0798 time to fit residues: 16.2746 Evaluate side-chains 132 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.143544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118106 restraints weight = 18836.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119870 restraints weight = 15048.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120659 restraints weight = 11263.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120900 restraints weight = 9498.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.121015 restraints weight = 9106.628| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8790 Z= 0.202 Angle : 0.850 13.870 12109 Z= 0.396 Chirality : 0.060 0.491 1367 Planarity : 0.004 0.045 1338 Dihedral : 17.584 159.164 1661 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.75 % Allowed : 18.50 % Favored : 77.75 % 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: -0.48 (0.28), residues: 916 helix: 1.59 (0.23), residues: 498 sheet: -2.58 (0.47), residues: 96 loop : -2.76 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 769 TYR 0.018 0.002 TYR A 963 PHE 0.023 0.002 PHE A 476 TRP 0.025 0.002 TRP A 915 HIS 0.005 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 8790) covalent geometry : angle 0.84996 / 0.40 (12109) hydrogen bonds : bond 0.04683 / 2.90 ( 439) hydrogen bonds : angle 4.72189 / 3.44 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6284 (tpt) cc_final: 0.5821 (tpt) REVERT: A 34 MET cc_start: 0.8116 (mmm) cc_final: 0.7878 (mmm) REVERT: A 159 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6776 (tp30) REVERT: A 335 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.6260 (m-10) REVERT: A 539 GLU cc_start: 0.4706 (tp30) cc_final: 0.3501 (tp30) REVERT: A 929 MET cc_start: 0.7276 (mtp) cc_final: 0.7030 (mtm) REVERT: A 940 ASN cc_start: 0.8025 (t0) cc_final: 0.7431 (p0) REVERT: A 948 ASP cc_start: 0.7356 (t0) cc_final: 0.7072 (t0) outliers start: 29 outliers final: 22 residues processed: 137 average time/residue: 0.0867 time to fit residues: 17.2842 Evaluate side-chains 135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.146542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.119719 restraints weight = 18471.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121302 restraints weight = 13750.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.122993 restraints weight = 10142.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.122987 restraints weight = 7742.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.123262 restraints weight = 7718.603| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8790 Z= 0.155 Angle : 0.810 13.685 12109 Z= 0.377 Chirality : 0.058 0.539 1367 Planarity : 0.004 0.034 1338 Dihedral : 17.550 163.784 1661 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.98 % Allowed : 19.40 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.34 (0.28), residues: 916 helix: 1.66 (0.23), residues: 499 sheet: -2.25 (0.50), residues: 86 loop : -2.73 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 769 TYR 0.016 0.002 TYR A 646 PHE 0.022 0.002 PHE A 743 TRP 0.042 0.003 TRP A 915 HIS 0.002 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 8790) covalent geometry : angle 0.80961 / 0.38 (12109) hydrogen bonds : bond 0.04300 / 2.68 ( 439) hydrogen bonds : angle 4.62059 / 3.36 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6235 (tpt) cc_final: 0.5809 (tpt) REVERT: A 34 MET cc_start: 0.8019 (mmm) cc_final: 0.7663 (mmm) REVERT: A 75 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7246 (mt) REVERT: A 159 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6717 (tp30) REVERT: A 335 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6561 (m-10) REVERT: A 940 ASN cc_start: 0.8099 (t0) cc_final: 0.7459 (p0) REVERT: A 948 ASP cc_start: 0.7301 (t0) cc_final: 0.7029 (t0) REVERT: A 1043 ARG cc_start: 0.6482 (mmt180) cc_final: 0.5245 (tpp80) outliers start: 23 outliers final: 16 residues processed: 133 average time/residue: 0.0805 time to fit residues: 15.7849 Evaluate side-chains 137 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN A 477 ASN A 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.147830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.120806 restraints weight = 18596.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122195 restraints weight = 13908.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124199 restraints weight = 10213.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.124127 restraints weight = 7776.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.124314 restraints weight = 7730.920| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8790 Z= 0.151 Angle : 0.796 12.903 12109 Z= 0.370 Chirality : 0.057 0.499 1367 Planarity : 0.004 0.034 1338 Dihedral : 17.534 166.302 1661 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.23 % Allowed : 19.02 % Favored : 77.75 % 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: -0.28 (0.28), residues: 916 helix: 1.69 (0.23), residues: 499 sheet: -2.13 (0.50), residues: 86 loop : -2.72 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 652 TYR 0.013 0.001 TYR A 406 PHE 0.024 0.002 PHE A 743 TRP 0.032 0.002 TRP A 915 HIS 0.004 0.001 HIS A 820 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 8790) covalent geometry : angle 0.79602 / 0.37 (12109) hydrogen bonds : bond 0.04228 / 2.64 ( 439) hydrogen bonds : angle 4.55089 / 3.32 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6240 (tpt) cc_final: 0.5832 (tpt) REVERT: A 34 MET cc_start: 0.8034 (mmm) cc_final: 0.7639 (mmm) REVERT: A 86 ASN cc_start: 0.8614 (p0) cc_final: 0.8409 (p0) REVERT: A 159 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6700 (tp30) REVERT: A 176 MET cc_start: 0.6217 (ppp) cc_final: 0.5888 (tmm) REVERT: A 335 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6552 (m-10) REVERT: A 929 MET cc_start: 0.7283 (mtp) cc_final: 0.6962 (mtm) REVERT: A 940 ASN cc_start: 0.7997 (t0) cc_final: 0.7314 (p0) REVERT: A 948 ASP cc_start: 0.7252 (t0) cc_final: 0.6968 (t0) REVERT: A 1043 ARG cc_start: 0.6415 (mmt180) cc_final: 0.5279 (tpp80) outliers start: 25 outliers final: 16 residues processed: 141 average time/residue: 0.0811 time to fit residues: 16.6989 Evaluate side-chains 132 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 890 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.145443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.118305 restraints weight = 18624.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.119883 restraints weight = 14136.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121044 restraints weight = 10201.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121317 restraints weight = 8198.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121411 restraints weight = 8066.688| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8790 Z= 0.196 Angle : 0.817 12.772 12109 Z= 0.382 Chirality : 0.059 0.458 1367 Planarity : 0.004 0.041 1338 Dihedral : 17.559 166.031 1661 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.59 % Allowed : 19.53 % Favored : 77.88 % 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: -0.28 (0.28), residues: 916 helix: 1.72 (0.23), residues: 499 sheet: -2.11 (0.51), residues: 86 loop : -2.78 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 918 TYR 0.013 0.002 TYR A 963 PHE 0.033 0.002 PHE A 807 TRP 0.031 0.002 TRP A 915 HIS 0.003 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 8790) covalent geometry : angle 0.81658 / 0.38 (12109) hydrogen bonds : bond 0.04330 / 2.73 ( 439) hydrogen bonds : angle 4.63064 / 3.37 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6288 (tpt) cc_final: 0.5859 (tpt) REVERT: A 34 MET cc_start: 0.8118 (mmm) cc_final: 0.7754 (mmm) REVERT: A 86 ASN cc_start: 0.8616 (p0) cc_final: 0.8414 (p0) REVERT: A 159 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6739 (tp30) REVERT: A 335 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6539 (m-10) REVERT: A 758 MET cc_start: 0.7867 (mmm) cc_final: 0.7508 (mmt) REVERT: A 929 MET cc_start: 0.7398 (mtp) cc_final: 0.7091 (mtm) REVERT: A 940 ASN cc_start: 0.7999 (t0) cc_final: 0.7320 (p0) REVERT: A 948 ASP cc_start: 0.7373 (t0) cc_final: 0.7113 (t0) REVERT: A 1043 ARG cc_start: 0.6476 (mmt180) cc_final: 0.5398 (tpp80) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.0767 time to fit residues: 14.9477 Evaluate side-chains 131 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 890 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.0040 chunk 12 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.145683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.118207 restraints weight = 18571.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.119783 restraints weight = 13317.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120665 restraints weight = 9990.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121205 restraints weight = 8820.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121344 restraints weight = 8046.789| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 8790 Z= 0.234 Angle : 1.076 59.200 12109 Z= 0.587 Chirality : 0.064 0.970 1367 Planarity : 0.004 0.059 1338 Dihedral : 17.559 166.166 1661 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.33 % Allowed : 20.18 % Favored : 77.49 % Cbeta Deviations : 0.11 % 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: -0.26 (0.28), residues: 916 helix: 1.74 (0.23), residues: 499 sheet: -2.09 (0.51), residues: 86 loop : -2.78 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 918 TYR 0.013 0.002 TYR A 406 PHE 0.028 0.002 PHE A 807 TRP 0.029 0.004 TRP A 915 HIS 0.003 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 ( 8790) covalent geometry : angle 1.07583 / 0.59 (12109) hydrogen bonds : bond 0.04389 / 2.78 ( 439) hydrogen bonds : angle 4.64843 / 3.38 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1338.67 seconds wall clock time: 24 minutes 9.42 seconds (1449.42 seconds total)