Starting phenix.real_space_refine on Sun Apr 5 01:45:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v43_64765/04_2026/9v43_64765.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v43_64765/04_2026/9v43_64765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v43_64765/04_2026/9v43_64765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v43_64765/04_2026/9v43_64765.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v43_64765/04_2026/9v43_64765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v43_64765/04_2026/9v43_64765.map" } resolution = 3.34 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= 0.002 sd= 0.036 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 54 5.49 5 S 29 5.16 5 C 4211 2.51 5 N 1167 2.21 5 O 1426 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6889 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1144 Classifications: {'RNA': 54} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 24, 'rna3p_pyr': 26} Link IDs: {'rna2p': 3, 'rna3p': 50} Chain breaks: 1 Chain: "B" Number of atoms: 5743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5743 Classifications: {'peptide': 712} Link IDs: {'PTRANS': 50, 'TRANS': 661} Chain breaks: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.59, per 1000 atoms: 0.23 Number of scatterers: 6889 At special positions: 0 Unit cell: (60.42, 71.02, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 29 16.00 P 54 15.00 O 1426 8.00 N 1167 7.00 C 4211 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: 0.74 Conformation dependent library (CDL) restraints added in 158.1 milliseconds 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1364 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 2 sheets defined 48.7% alpha, 3.7% beta 24 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 794 through 798 removed outlier: 3.594A pdb=" N THR B 798 " --> pdb=" O PRO B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 855 Processing helix chain 'B' and resid 895 through 904 removed outlier: 5.241A pdb=" N GLU B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B 902 " --> pdb=" O GLU B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 976 Processing helix chain 'B' and resid 1017 through 1029 Processing helix chain 'B' and resid 1034 through 1038 Processing helix chain 'B' and resid 1044 through 1074 Proline residue: B1055 - end of helix removed outlier: 3.642A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B1070 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1293 through 1302 Processing helix chain 'B' and resid 1314 through 1335 Processing helix chain 'B' and resid 1339 through 1364 removed outlier: 4.696A pdb=" N CYS B1354 " --> pdb=" O LYS B1350 " (cutoff:3.500A) Processing helix chain 'B' and resid 1364 through 1369 removed outlier: 4.196A pdb=" N ARG B1368 " --> pdb=" O GLY B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1380 removed outlier: 3.594A pdb=" N ASN B1379 " --> pdb=" O ASP B1375 " (cutoff:3.500A) Processing helix chain 'B' and resid 1555 through 1586 removed outlier: 6.831A pdb=" N GLU B1576 " --> pdb=" O THR B1572 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ARG B1577 " --> pdb=" O SER B1573 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B1578 " --> pdb=" O CYS B1574 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B1579 " --> pdb=" O GLY B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1662 through 1674 removed outlier: 3.647A pdb=" N ASN B1668 " --> pdb=" O SER B1664 " (cutoff:3.500A) Processing helix chain 'B' and resid 1680 through 1688 Processing helix chain 'B' and resid 1701 through 1723 Processing helix chain 'B' and resid 1728 through 1741 Processing helix chain 'B' and resid 1741 through 1752 Processing helix chain 'B' and resid 1754 through 1758 Processing helix chain 'B' and resid 1762 through 1776 removed outlier: 3.786A pdb=" N PHE B1766 " --> pdb=" O SER B1762 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS B1767 " --> pdb=" O PRO B1763 " (cutoff:3.500A) Processing helix chain 'B' and resid 1805 through 1823 removed outlier: 4.482A pdb=" N GLY B1809 " --> pdb=" O PRO B1805 " (cutoff:3.500A) Processing helix chain 'B' and resid 1827 through 1835 Processing helix chain 'B' and resid 1838 through 1848 Processing helix chain 'B' and resid 1852 through 1861 Processing helix chain 'B' and resid 1897 through 1912 Processing sheet with id=AA1, first strand: chain 'B' and resid 769 through 770 removed outlier: 3.580A pdb=" N TYR B 769 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 806 " --> pdb=" O TYR B 769 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 879 " --> pdb=" O GLY B 803 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 773 through 776 removed outlier: 3.802A pdb=" N PHE B 816 " --> pdb=" O ILE B 827 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 717 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1926 1.34 - 1.46: 1545 1.46 - 1.58: 3544 1.58 - 1.70: 106 1.70 - 1.81: 42 Bond restraints: 7163 Sorted by residual: bond pdb=" CB ASP B1713 " pdb=" CG ASP B1713 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.12e+00 bond pdb=" N VAL B 736 " pdb=" CA VAL B 736 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" CB LYS B 895 " pdb=" CG LYS B 895 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.34e+00 bond pdb=" CA PHE B1374 " pdb=" C PHE B1374 " ideal model delta sigma weight residual 1.518 1.575 -0.057 4.01e-02 6.22e+02 2.03e+00 bond pdb=" CB VAL B 931 " pdb=" CG2 VAL B 931 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 ... (remaining 7158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 9637 2.08 - 4.16: 268 4.16 - 6.24: 50 6.24 - 8.32: 9 8.32 - 10.41: 1 Bond angle restraints: 9965 Sorted by residual: angle pdb=" CB LYS B1759 " pdb=" CG LYS B1759 " pdb=" CD LYS B1759 " ideal model delta sigma weight residual 111.30 121.71 -10.41 2.30e+00 1.89e-01 2.05e+01 angle pdb=" CA LYS B 895 " pdb=" CB LYS B 895 " pdb=" CG LYS B 895 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CA LYS B1759 " pdb=" CB LYS B1759 " pdb=" CG LYS B1759 " ideal model delta sigma weight residual 114.10 121.47 -7.37 2.00e+00 2.50e-01 1.36e+01 angle pdb=" C SER B 742 " pdb=" CA SER B 742 " pdb=" CB SER B 742 " ideal model delta sigma weight residual 115.89 111.11 4.78 1.32e+00 5.74e-01 1.31e+01 angle pdb=" C PHE B 968 " pdb=" CA PHE B 968 " pdb=" CB PHE B 968 " ideal model delta sigma weight residual 115.89 111.15 4.74 1.32e+00 5.74e-01 1.29e+01 ... (remaining 9960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.26: 4078 31.26 - 62.52: 284 62.52 - 93.79: 44 93.79 - 125.05: 3 125.05 - 156.31: 2 Dihedral angle restraints: 4411 sinusoidal: 2300 harmonic: 2111 Sorted by residual: dihedral pdb=" O4' U A 63 " pdb=" C1' U A 63 " pdb=" N1 U A 63 " pdb=" C2 U A 63 " ideal model delta sinusoidal sigma weight residual -128.00 28.31 -156.31 1 1.70e+01 3.46e-03 6.36e+01 dihedral pdb=" O4' U A 1 " pdb=" C1' U A 1 " pdb=" N1 U A 1 " pdb=" C2 U A 1 " ideal model delta sinusoidal sigma weight residual -128.00 22.83 -150.83 1 1.70e+01 3.46e-03 6.22e+01 dihedral pdb=" CA HIS B1041 " pdb=" C HIS B1041 " pdb=" N PRO B1042 " pdb=" CA PRO B1042 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 4408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 902 0.045 - 0.091: 192 0.091 - 0.136: 49 0.136 - 0.182: 9 0.182 - 0.227: 1 Chirality restraints: 1153 Sorted by residual: chirality pdb=" CG LEU B 865 " pdb=" CB LEU B 865 " pdb=" CD1 LEU B 865 " pdb=" CD2 LEU B 865 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA TYR B1570 " pdb=" N TYR B1570 " pdb=" C TYR B1570 " pdb=" CB TYR B1570 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA ILE B 810 " pdb=" N ILE B 810 " pdb=" C ILE B 810 " pdb=" CB ILE B 810 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 1150 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 933 " 0.080 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO B 934 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 934 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 934 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B1835 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO B1836 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B1836 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B1836 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B1861 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO B1862 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B1862 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B1862 " -0.038 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 107 2.59 - 3.17: 6419 3.17 - 3.75: 12240 3.75 - 4.32: 16586 4.32 - 4.90: 25294 Nonbonded interactions: 60646 Sorted by model distance: nonbonded pdb=" OG1 THR B 799 " pdb=" OD1 ASN B 882 " model vdw 2.014 3.040 nonbonded pdb=" O2' A A 22 " pdb=" OD2 ASP B1709 " model vdw 2.066 3.040 nonbonded pdb=" OG SER B1826 " pdb=" OG1 THR B1829 " model vdw 2.068 3.040 nonbonded pdb=" O GLY B1341 " pdb=" OG SER B1344 " model vdw 2.093 3.040 nonbonded pdb=" O2' G A 13 " pdb=" O VAL B 736 " model vdw 2.115 3.040 ... (remaining 60641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.330 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 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 : 0.005 0.057 7163 Z= 0.202 Angle : 0.849 10.405 9965 Z= 0.432 Chirality : 0.042 0.227 1153 Planarity : 0.008 0.120 1074 Dihedral : 19.444 156.308 3047 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.47 % Allowed : 23.39 % Favored : 76.14 % 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: -1.87 (0.31), residues: 702 helix: 0.09 (0.29), residues: 306 sheet: -3.16 (1.10), residues: 20 loop : -2.38 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 906 TYR 0.037 0.002 TYR B1675 PHE 0.016 0.002 PHE B 945 TRP 0.009 0.001 TRP B1048 HIS 0.008 0.002 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 7163) covalent geometry : angle 0.84945 ( 9965) hydrogen bonds : bond 0.13000 ( 303) hydrogen bonds : angle 6.64373 ( 821) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 960 PHE cc_start: 0.4737 (OUTLIER) cc_final: 0.4295 (t80) outliers start: 3 outliers final: 1 residues processed: 91 average time/residue: 0.0987 time to fit residues: 11.3075 Evaluate side-chains 81 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 1307 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.172066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.155123 restraints weight = 18864.032| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 3.16 r_work: 0.4521 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7163 Z= 0.182 Angle : 0.743 10.196 9965 Z= 0.369 Chirality : 0.042 0.188 1153 Planarity : 0.007 0.076 1074 Dihedral : 18.346 153.647 1612 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.92 % Allowed : 19.00 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.31), residues: 702 helix: 0.09 (0.29), residues: 312 sheet: -3.36 (0.97), residues: 20 loop : -2.16 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B1703 TYR 0.029 0.002 TYR B1570 PHE 0.020 0.002 PHE B 787 TRP 0.007 0.001 TRP B1048 HIS 0.005 0.001 HIS B1549 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7163) covalent geometry : angle 0.74305 ( 9965) hydrogen bonds : bond 0.05581 ( 303) hydrogen bonds : angle 5.68357 ( 821) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 960 PHE cc_start: 0.4911 (OUTLIER) cc_final: 0.4385 (t80) REVERT: B 1038 CYS cc_start: 0.7169 (p) cc_final: 0.6775 (p) REVERT: B 1570 TYR cc_start: 0.3982 (p90) cc_final: 0.3602 (p90) REVERT: B 1702 GLN cc_start: 0.3378 (OUTLIER) cc_final: 0.2834 (tm-30) REVERT: B 1713 ASP cc_start: 0.6530 (p0) cc_final: 0.6226 (p0) REVERT: B 1813 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6961 (mt-10) outliers start: 25 outliers final: 6 residues processed: 105 average time/residue: 0.0991 time to fit residues: 13.3287 Evaluate side-chains 86 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1315 LEU Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1702 GLN Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1849 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1702 GLN B1719 HIS B1742 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.174415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.157441 restraints weight = 17880.450| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 3.11 r_work: 0.4557 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7163 Z= 0.154 Angle : 0.688 9.772 9965 Z= 0.345 Chirality : 0.041 0.170 1153 Planarity : 0.006 0.062 1074 Dihedral : 18.184 154.305 1611 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.61 % Allowed : 20.57 % Favored : 75.82 % 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: -1.62 (0.31), residues: 702 helix: 0.16 (0.29), residues: 313 sheet: -3.79 (0.78), residues: 25 loop : -2.04 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 746 TYR 0.022 0.002 TYR B1570 PHE 0.022 0.002 PHE B 787 TRP 0.008 0.001 TRP B1831 HIS 0.006 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7163) covalent geometry : angle 0.68770 ( 9965) hydrogen bonds : bond 0.05087 ( 303) hydrogen bonds : angle 5.47812 ( 821) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 944 ARG cc_start: 0.4471 (ptp-170) cc_final: 0.3738 (ptp-170) REVERT: B 960 PHE cc_start: 0.4858 (OUTLIER) cc_final: 0.4361 (t80) REVERT: B 1038 CYS cc_start: 0.7105 (p) cc_final: 0.6750 (p) REVERT: B 1380 TRP cc_start: 0.2850 (OUTLIER) cc_final: 0.1227 (t60) REVERT: B 1813 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6805 (mt-10) outliers start: 23 outliers final: 9 residues processed: 102 average time/residue: 0.0969 time to fit residues: 12.6056 Evaluate side-chains 97 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1380 TRP Chi-restraints excluded: chain B residue 1744 ILE Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1849 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 20 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.174117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.156795 restraints weight = 17828.414| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 3.15 r_work: 0.4546 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7163 Z= 0.155 Angle : 0.682 10.120 9965 Z= 0.342 Chirality : 0.040 0.162 1153 Planarity : 0.006 0.063 1074 Dihedral : 18.091 155.712 1611 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.61 % Allowed : 22.61 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.31), residues: 702 helix: 0.23 (0.29), residues: 314 sheet: -3.82 (0.74), residues: 25 loop : -2.01 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 745 TYR 0.031 0.002 TYR B1757 PHE 0.018 0.002 PHE B 802 TRP 0.004 0.001 TRP B1024 HIS 0.006 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7163) covalent geometry : angle 0.68171 ( 9965) hydrogen bonds : bond 0.05081 ( 303) hydrogen bonds : angle 5.49353 ( 821) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 906 ARG cc_start: 0.4780 (tpp80) cc_final: 0.4514 (tpp-160) REVERT: B 944 ARG cc_start: 0.4364 (ptp-170) cc_final: 0.3635 (ptp-170) REVERT: B 960 PHE cc_start: 0.4887 (OUTLIER) cc_final: 0.4456 (t80) REVERT: B 1018 GLU cc_start: 0.5230 (OUTLIER) cc_final: 0.4934 (pp20) REVERT: B 1019 LYS cc_start: 0.2590 (tppt) cc_final: 0.1950 (tppt) REVERT: B 1038 CYS cc_start: 0.7104 (p) cc_final: 0.6754 (p) REVERT: B 1380 TRP cc_start: 0.2954 (OUTLIER) cc_final: 0.1174 (t60) REVERT: B 1702 GLN cc_start: 0.3138 (OUTLIER) cc_final: 0.2630 (tm-30) REVERT: B 1813 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6748 (mt-10) outliers start: 23 outliers final: 11 residues processed: 104 average time/residue: 0.0936 time to fit residues: 12.5518 Evaluate side-chains 97 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1315 LEU Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1380 TRP Chi-restraints excluded: chain B residue 1702 GLN Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 59 optimal weight: 0.0770 chunk 31 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.175098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.157935 restraints weight = 17973.374| |-----------------------------------------------------------------------------| r_work (start): 0.4696 rms_B_bonded: 3.13 r_work: 0.4577 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7163 Z= 0.143 Angle : 0.674 10.474 9965 Z= 0.338 Chirality : 0.040 0.156 1153 Planarity : 0.006 0.064 1074 Dihedral : 17.969 156.646 1611 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.92 % Allowed : 22.29 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.32), residues: 702 helix: 0.38 (0.29), residues: 314 sheet: -3.79 (0.72), residues: 25 loop : -1.96 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1839 TYR 0.039 0.002 TYR B1834 PHE 0.024 0.002 PHE B 787 TRP 0.007 0.001 TRP B1024 HIS 0.007 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7163) covalent geometry : angle 0.67435 ( 9965) hydrogen bonds : bond 0.04873 ( 303) hydrogen bonds : angle 5.38880 ( 821) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 837 MET cc_start: 0.4356 (OUTLIER) cc_final: 0.4072 (tpt) REVERT: B 944 ARG cc_start: 0.4269 (ptp-170) cc_final: 0.3534 (ptp-170) REVERT: B 960 PHE cc_start: 0.4811 (OUTLIER) cc_final: 0.4317 (t80) REVERT: B 1038 CYS cc_start: 0.7046 (p) cc_final: 0.6702 (p) REVERT: B 1380 TRP cc_start: 0.2863 (OUTLIER) cc_final: 0.1234 (t60) REVERT: B 1582 PHE cc_start: 0.3337 (t80) cc_final: 0.2986 (t80) REVERT: B 1813 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6755 (mt-10) outliers start: 25 outliers final: 13 residues processed: 102 average time/residue: 0.0902 time to fit residues: 12.0424 Evaluate side-chains 97 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1380 TRP Chi-restraints excluded: chain B residue 1566 LEU Chi-restraints excluded: chain B residue 1712 LEU Chi-restraints excluded: chain B residue 1810 ASP Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 20 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4942 r_free = 0.4942 target = 0.174505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.157669 restraints weight = 18275.366| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 3.13 r_work: 0.4570 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7163 Z= 0.149 Angle : 0.683 10.605 9965 Z= 0.341 Chirality : 0.040 0.174 1153 Planarity : 0.006 0.064 1074 Dihedral : 17.966 157.609 1611 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.87 % Allowed : 22.14 % Favored : 73.00 % 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: -1.43 (0.32), residues: 702 helix: 0.37 (0.29), residues: 314 sheet: -3.75 (0.65), residues: 35 loop : -1.92 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1020 TYR 0.038 0.002 TYR B1834 PHE 0.016 0.002 PHE B1582 TRP 0.010 0.001 TRP B1024 HIS 0.008 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7163) covalent geometry : angle 0.68257 ( 9965) hydrogen bonds : bond 0.04872 ( 303) hydrogen bonds : angle 5.34030 ( 821) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 906 ARG cc_start: 0.4614 (tpp80) cc_final: 0.4220 (tpp-160) REVERT: B 960 PHE cc_start: 0.4819 (OUTLIER) cc_final: 0.4344 (t80) REVERT: B 1038 CYS cc_start: 0.7052 (p) cc_final: 0.6698 (p) REVERT: B 1380 TRP cc_start: 0.2939 (OUTLIER) cc_final: 0.1156 (t60) REVERT: B 1582 PHE cc_start: 0.3482 (t80) cc_final: 0.3222 (t80) REVERT: B 1813 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6879 (mt-10) outliers start: 31 outliers final: 19 residues processed: 106 average time/residue: 0.0920 time to fit residues: 12.8212 Evaluate side-chains 102 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 783 ASP Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1380 TRP Chi-restraints excluded: chain B residue 1566 LEU Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1712 LEU Chi-restraints excluded: chain B residue 1744 ILE Chi-restraints excluded: chain B residue 1810 ASP Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 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 = 0.4936 r_free = 0.4936 target = 0.173472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.156656 restraints weight = 18525.148| |-----------------------------------------------------------------------------| r_work (start): 0.4675 rms_B_bonded: 3.13 r_work: 0.4554 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7163 Z= 0.158 Angle : 0.706 11.064 9965 Z= 0.352 Chirality : 0.041 0.244 1153 Planarity : 0.006 0.063 1074 Dihedral : 17.965 158.743 1611 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.45 % Allowed : 23.86 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.32), residues: 702 helix: 0.38 (0.29), residues: 314 sheet: -3.74 (0.64), residues: 34 loop : -1.94 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1020 TYR 0.040 0.002 TYR B1834 PHE 0.037 0.002 PHE B 802 TRP 0.005 0.001 TRP B1024 HIS 0.007 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7163) covalent geometry : angle 0.70556 ( 9965) hydrogen bonds : bond 0.04907 ( 303) hydrogen bonds : angle 5.40170 ( 821) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 790 ARG cc_start: 0.2496 (mmt90) cc_final: 0.1868 (tmt170) REVERT: B 935 ARG cc_start: 0.4112 (OUTLIER) cc_final: 0.3671 (tpp-160) REVERT: B 960 PHE cc_start: 0.4868 (OUTLIER) cc_final: 0.4388 (t80) REVERT: B 1038 CYS cc_start: 0.7161 (p) cc_final: 0.6801 (p) REVERT: B 1380 TRP cc_start: 0.3141 (OUTLIER) cc_final: 0.1258 (t60) REVERT: B 1570 TYR cc_start: 0.4009 (p90) cc_final: 0.3697 (p90) REVERT: B 1813 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6775 (mt-10) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 0.0993 time to fit residues: 13.2797 Evaluate side-chains 98 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 783 ASP Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 935 ARG Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1380 TRP Chi-restraints excluded: chain B residue 1712 LEU Chi-restraints excluded: chain B residue 1810 ASP Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1832 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.171603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.154573 restraints weight = 18672.992| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 3.16 r_work: 0.4527 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7163 Z= 0.183 Angle : 0.741 11.156 9965 Z= 0.374 Chirality : 0.044 0.343 1153 Planarity : 0.006 0.065 1074 Dihedral : 18.056 160.271 1611 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.55 % Favored : 92.31 % Rotamer: Outliers : 4.08 % Allowed : 23.70 % Favored : 72.21 % 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: -1.66 (0.31), residues: 702 helix: 0.13 (0.28), residues: 314 sheet: -4.11 (0.60), residues: 37 loop : -1.94 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1839 TYR 0.043 0.002 TYR B1834 PHE 0.030 0.002 PHE B 896 TRP 0.005 0.001 TRP B1380 HIS 0.008 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7163) covalent geometry : angle 0.74064 ( 9965) hydrogen bonds : bond 0.05193 ( 303) hydrogen bonds : angle 5.57525 ( 821) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 790 ARG cc_start: 0.2786 (mmt90) cc_final: 0.1911 (tmt170) REVERT: B 891 ASP cc_start: 0.7378 (m-30) cc_final: 0.7083 (m-30) REVERT: B 960 PHE cc_start: 0.4870 (OUTLIER) cc_final: 0.4358 (t80) REVERT: B 1038 CYS cc_start: 0.7241 (p) cc_final: 0.6844 (p) REVERT: B 1380 TRP cc_start: 0.3340 (OUTLIER) cc_final: 0.1267 (t60) REVERT: B 1813 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6920 (mt-10) outliers start: 26 outliers final: 16 residues processed: 105 average time/residue: 0.0934 time to fit residues: 12.5432 Evaluate side-chains 101 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 783 ASP Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1380 TRP Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1712 LEU Chi-restraints excluded: chain B residue 1810 ASP Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Chi-restraints excluded: chain B residue 1912 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4931 r_free = 0.4931 target = 0.173390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.156178 restraints weight = 18033.268| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 3.16 r_work: 0.4550 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7163 Z= 0.159 Angle : 0.735 11.062 9965 Z= 0.367 Chirality : 0.042 0.356 1153 Planarity : 0.006 0.064 1074 Dihedral : 18.008 164.045 1611 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.26 % Favored : 92.59 % Rotamer: Outliers : 3.45 % Allowed : 25.27 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.31), residues: 702 helix: 0.24 (0.29), residues: 316 sheet: -3.84 (0.63), residues: 34 loop : -1.97 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1577 TYR 0.044 0.002 TYR B1834 PHE 0.024 0.002 PHE B 802 TRP 0.006 0.001 TRP B1024 HIS 0.008 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7163) covalent geometry : angle 0.73521 ( 9965) hydrogen bonds : bond 0.04939 ( 303) hydrogen bonds : angle 5.51470 ( 821) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 891 ASP cc_start: 0.7314 (m-30) cc_final: 0.7112 (m-30) REVERT: B 960 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.4397 (t80) REVERT: B 1038 CYS cc_start: 0.7193 (p) cc_final: 0.6783 (p) REVERT: B 1380 TRP cc_start: 0.3193 (OUTLIER) cc_final: 0.1123 (t60) REVERT: B 1570 TYR cc_start: 0.3576 (p90) cc_final: 0.3122 (p90) REVERT: B 1813 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6889 (mt-10) outliers start: 22 outliers final: 17 residues processed: 99 average time/residue: 0.0883 time to fit residues: 11.4593 Evaluate side-chains 99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 783 ASP Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1315 LEU Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1380 TRP Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1581 LEU Chi-restraints excluded: chain B residue 1712 LEU Chi-restraints excluded: chain B residue 1810 ASP Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Chi-restraints excluded: chain B residue 1912 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.4946 r_free = 0.4946 target = 0.174722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.157743 restraints weight = 17992.102| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 3.11 r_work: 0.4571 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7163 Z= 0.154 Angle : 0.744 11.232 9965 Z= 0.372 Chirality : 0.043 0.384 1153 Planarity : 0.006 0.065 1074 Dihedral : 18.007 167.318 1611 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.98 % Favored : 92.88 % Rotamer: Outliers : 3.30 % Allowed : 25.12 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.32), residues: 702 helix: 0.34 (0.29), residues: 316 sheet: -4.03 (0.57), residues: 37 loop : -1.92 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1577 TYR 0.044 0.002 TYR B1834 PHE 0.027 0.002 PHE B1582 TRP 0.008 0.001 TRP B1024 HIS 0.008 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7163) covalent geometry : angle 0.74394 ( 9965) hydrogen bonds : bond 0.04863 ( 303) hydrogen bonds : angle 5.45607 ( 821) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1404 Ramachandran restraints generated. 702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 960 PHE cc_start: 0.4951 (OUTLIER) cc_final: 0.4395 (t80) REVERT: B 1038 CYS cc_start: 0.7177 (p) cc_final: 0.6787 (p) REVERT: B 1380 TRP cc_start: 0.3145 (OUTLIER) cc_final: 0.1116 (t60) REVERT: B 1813 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6728 (mt-10) outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 0.0981 time to fit residues: 12.3289 Evaluate side-chains 97 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 783 ASP Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1315 LEU Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1380 TRP Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1581 LEU Chi-restraints excluded: chain B residue 1810 ASP Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Chi-restraints excluded: chain B residue 1912 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 = 0.4965 r_free = 0.4965 target = 0.176469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.159475 restraints weight = 17962.698| |-----------------------------------------------------------------------------| r_work (start): 0.4707 rms_B_bonded: 3.12 r_work: 0.4583 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7163 Z= 0.153 Angle : 0.751 11.100 9965 Z= 0.375 Chirality : 0.042 0.384 1153 Planarity : 0.006 0.062 1074 Dihedral : 17.976 169.583 1611 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 3.14 % Allowed : 26.69 % Favored : 70.17 % 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: -1.48 (0.31), residues: 702 helix: 0.38 (0.29), residues: 314 sheet: -4.09 (0.56), residues: 37 loop : -1.95 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1020 TYR 0.044 0.002 TYR B1834 PHE 0.023 0.002 PHE B1582 TRP 0.008 0.001 TRP B1024 HIS 0.008 0.001 HIS B1325 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7163) covalent geometry : angle 0.75117 ( 9965) hydrogen bonds : bond 0.04928 ( 303) hydrogen bonds : angle 5.42253 ( 821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1667.42 seconds wall clock time: 29 minutes 24.65 seconds (1764.65 seconds total)