Starting phenix.real_space_refine on Thu Jul 2 06:08:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v43_64765/07_2026/9v43_64765.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v43_64765/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9v43_64765/07_2026/9v43_64765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v43_64765/07_2026/9v43_64765.map" model { file = "/net/cci-nas-00/data/ceres_data/9v43_64765/07_2026/9v43_64765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v43_64765/07_2026/9v43_64765.cif" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 1.38, per 1000 atoms: 0.20 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: 0.59 Conformation dependent library (CDL) restraints added in 289.9 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: 0.72 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: 1.08 Time building geometry restraints manager: 0.75 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=" C2 U A 20 " pdb=" N3 U A 20 " ideal model delta sigma weight residual 1.373 1.390 -0.017 7.00e-03 2.04e+04 5.97e+00 bond pdb=" N1 U A 20 " pdb=" C2 U A 20 " ideal model delta sigma weight residual 1.381 1.397 -0.016 9.00e-03 1.23e+04 3.17e+00 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=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.90e+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 ... (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=" O4 U A 20 " pdb=" C4 U A 20 " pdb=" C5 U A 20 " ideal model delta sigma weight residual 125.90 122.73 3.17 6.00e-01 2.78e+00 2.79e+01 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=" N3 U A 20 " pdb=" C4 U A 20 " pdb=" O4 U A 20 " ideal model delta sigma weight residual 119.40 122.46 -3.06 7.00e-01 2.04e+00 1.92e+01 angle pdb=" N1 C A 21 " pdb=" C6 C A 21 " pdb=" C5 C A 21 " ideal model delta sigma weight residual 121.00 123.03 -2.03 5.00e-01 4.00e+00 1.65e+01 angle pdb=" C1' U A 20 " pdb=" N1 U A 20 " pdb=" C2 U A 20 " ideal model delta sigma weight residual 117.70 122.57 -4.87 1.20e+00 6.94e-01 1.65e+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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.190 Find NCS groups from input model: 0.030 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 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= 0.225 Angle : 0.850 10.405 9965 Z= 0.505 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/Z covalent geometry : bond 0.00466 / 0.23 ( 7163) covalent geometry : angle 0.84951 / 0.50 ( 9965) hydrogen bonds : bond 0.13000 / 13.23 ( 303) hydrogen bonds : angle 6.64373 / 7.58 ( 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 : 0.138 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: 0.0926 time to fit residues: 10.5452 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 : 0.183 ------------------------------------------------------------------------------- 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... B1702 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 = 0.172324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.155276 restraints weight = 18826.169| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 3.19 r_work: 0.4525 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7163 Z= 0.190 Angle : 0.758 11.502 9965 Z= 0.386 Chirality : 0.043 0.170 1153 Planarity : 0.007 0.071 1074 Dihedral : 18.397 157.438 1612 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.30 % Allowed : 19.15 % Favored : 77.55 % 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: -1.78 (0.31), residues: 702 helix: 0.05 (0.28), residues: 311 sheet: -3.29 (0.97), residues: 20 loop : -2.23 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 788 TYR 0.023 0.002 TYR B1570 PHE 0.020 0.002 PHE B 787 TRP 0.008 0.001 TRP B1048 HIS 0.006 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 7163) covalent geometry : angle 0.75817 / 0.39 ( 9965) hydrogen bonds : bond 0.06428 / 7.28 ( 303) hydrogen bonds : angle 5.71327 / 6.61 ( 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 104 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 960 PHE cc_start: 0.4898 (OUTLIER) cc_final: 0.4381 (t80) REVERT: B 1038 CYS cc_start: 0.7254 (p) cc_final: 0.6929 (p) REVERT: B 1582 PHE cc_start: 0.3417 (t80) cc_final: 0.2966 (t80) REVERT: B 1702 GLN cc_start: 0.3352 (OUTLIER) cc_final: 0.2829 (tm-30) REVERT: B 1713 ASP cc_start: 0.6478 (p0) cc_final: 0.6272 (p0) outliers start: 21 outliers final: 5 residues processed: 100 average time/residue: 0.0840 time to fit residues: 10.8346 Evaluate side-chains 85 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 1037 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 1849 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1719 HIS B1742 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.173364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.156747 restraints weight = 17927.538| |-----------------------------------------------------------------------------| r_work (start): 0.4662 rms_B_bonded: 3.09 r_work: 0.4540 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7163 Z= 0.182 Angle : 0.732 9.842 9965 Z= 0.375 Chirality : 0.043 0.212 1153 Planarity : 0.007 0.063 1074 Dihedral : 18.414 158.587 1611 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.83 % Allowed : 22.61 % Favored : 74.57 % 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: -0.05 (0.29), residues: 311 sheet: -3.96 (0.72), residues: 25 loop : -2.17 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 789 TYR 0.057 0.002 TYR B1757 PHE 0.018 0.002 PHE B 787 TRP 0.010 0.002 TRP B1831 HIS 0.004 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 7163) covalent geometry : angle 0.73248 / 0.38 ( 9965) hydrogen bonds : bond 0.05979 / 6.78 ( 303) hydrogen bonds : angle 5.70571 / 6.56 ( 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 98 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 960 PHE cc_start: 0.4866 (OUTLIER) cc_final: 0.4363 (t80) REVERT: B 1038 CYS cc_start: 0.7210 (p) cc_final: 0.6827 (p) REVERT: B 1570 TYR cc_start: 0.3800 (p90) cc_final: 0.3483 (p90) REVERT: B 1683 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5516 (mt) REVERT: B 1813 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7035 (mt-10) outliers start: 18 outliers final: 7 residues processed: 94 average time/residue: 0.1003 time to fit residues: 12.3311 Evaluate side-chains 88 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL Chi-restraints excluded: chain B residue 1683 LEU Chi-restraints excluded: chain B residue 1744 ILE Chi-restraints excluded: chain B residue 1813 GLU 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: 0.6980 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.172805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.155995 restraints weight = 18686.007| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 3.12 r_work: 0.4544 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7163 Z= 0.161 Angle : 0.689 9.325 9965 Z= 0.356 Chirality : 0.041 0.168 1153 Planarity : 0.006 0.063 1074 Dihedral : 18.360 162.414 1611 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.45 % Allowed : 23.39 % Favored : 73.16 % 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: -1.76 (0.31), residues: 702 helix: 0.02 (0.28), residues: 312 sheet: -3.80 (0.73), residues: 25 loop : -2.10 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1839 TYR 0.033 0.002 TYR B1834 PHE 0.037 0.002 PHE B 787 TRP 0.006 0.002 TRP B1024 HIS 0.005 0.001 HIS B1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7163) covalent geometry : angle 0.68886 / 0.36 ( 9965) hydrogen bonds : bond 0.05638 / 6.49 ( 303) hydrogen bonds : angle 5.59284 / 6.45 ( 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 105 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 790 ARG cc_start: 0.2332 (mmt90) cc_final: 0.1823 (tmt170) REVERT: B 944 ARG cc_start: 0.4487 (ptp-170) cc_final: 0.3862 (ptp-170) REVERT: B 960 PHE cc_start: 0.4886 (OUTLIER) cc_final: 0.4376 (t80) REVERT: B 1038 CYS cc_start: 0.7235 (p) cc_final: 0.6826 (p) REVERT: B 1813 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6895 (mt-10) outliers start: 22 outliers final: 10 residues processed: 97 average time/residue: 0.1009 time to fit residues: 12.7601 Evaluate side-chains 92 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1037 LEU Chi-restraints excluded: chain B residue 1354 CYS Chi-restraints excluded: chain B residue 1378 VAL 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=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: 2.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.172109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.154532 restraints weight = 18044.336| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 3.15 r_work: 0.4521 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.1954 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= 0.174 Angle : 0.692 9.771 9965 Z= 0.358 Chirality : 0.041 0.166 1153 Planarity : 0.006 0.065 1074 Dihedral : 18.350 165.870 1611 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.24 % Allowed : 22.76 % 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: -1.79 (0.31), residues: 702 helix: -0.08 (0.29), residues: 311 sheet: -3.79 (0.72), residues: 25 loop : -2.04 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1839 TYR 0.049 0.003 TYR B1834 PHE 0.027 0.002 PHE B 787 TRP 0.005 0.001 TRP B1024 HIS 0.006 0.001 HIS B1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 7163) covalent geometry : angle 0.69220 / 0.36 ( 9965) hydrogen bonds : bond 0.05774 / 6.50 ( 303) hydrogen bonds : angle 5.70138 / 6.48 ( 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 113 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 790 ARG cc_start: 0.2349 (mmt90) cc_final: 0.1898 (tmt170) REVERT: B 944 ARG cc_start: 0.4624 (ptp-170) cc_final: 0.4042 (ptp-170) REVERT: B 960 PHE cc_start: 0.4920 (OUTLIER) cc_final: 0.4421 (t80) REVERT: B 1038 CYS cc_start: 0.7310 (p) cc_final: 0.6922 (p) REVERT: B 1380 TRP cc_start: 0.2890 (OUTLIER) cc_final: 0.1155 (t60) REVERT: B 1813 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6953 (mt-10) outliers start: 27 outliers final: 11 residues processed: 108 average time/residue: 0.1049 time to fit residues: 14.6594 Evaluate side-chains 96 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1712 LEU 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: 2.9990 chunk 19 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 62 optimal weight: 0.0570 chunk 59 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.173288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.156056 restraints weight = 18733.213| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 3.15 r_work: 0.4544 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.2099 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= 0.156 Angle : 0.697 10.882 9965 Z= 0.356 Chirality : 0.041 0.199 1153 Planarity : 0.006 0.064 1074 Dihedral : 18.309 168.921 1611 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.30 % Allowed : 23.86 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.32), residues: 702 helix: -0.01 (0.29), residues: 314 sheet: -3.90 (0.71), residues: 25 loop : -1.92 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1839 TYR 0.049 0.002 TYR B1834 PHE 0.030 0.002 PHE B 802 TRP 0.004 0.001 TRP B1024 HIS 0.007 0.001 HIS B1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7163) covalent geometry : angle 0.69654 / 0.36 ( 9965) hydrogen bonds : bond 0.05510 / 6.24 ( 303) hydrogen bonds : angle 5.56091 / 6.34 ( 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 103 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 790 ARG cc_start: 0.2263 (mmt90) cc_final: 0.1830 (tmt170) REVERT: B 840 LEU cc_start: 0.8235 (tt) cc_final: 0.8009 (tt) REVERT: B 906 ARG cc_start: 0.4700 (tpp80) cc_final: 0.4169 (tpp-160) REVERT: B 944 ARG cc_start: 0.4545 (ptp-170) cc_final: 0.3944 (ptp-170) REVERT: B 960 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.4407 (t80) REVERT: B 1038 CYS cc_start: 0.7255 (p) cc_final: 0.6889 (p) REVERT: B 1380 TRP cc_start: 0.2917 (OUTLIER) cc_final: 0.1202 (t60) REVERT: B 1813 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6927 (mt-10) outliers start: 21 outliers final: 12 residues processed: 97 average time/residue: 0.0947 time to fit residues: 11.9699 Evaluate side-chains 97 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1033 LEU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1315 LEU Chi-restraints excluded: chain B residue 1346 MET 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 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: 2.9990 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 48 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.172530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.155934 restraints weight = 18659.349| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 3.15 r_work: 0.4554 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7163 Z= 0.153 Angle : 0.692 10.938 9965 Z= 0.355 Chirality : 0.041 0.160 1153 Planarity : 0.006 0.066 1074 Dihedral : 18.260 171.644 1611 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.92 % Allowed : 23.08 % 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: -1.66 (0.31), residues: 702 helix: 0.03 (0.28), residues: 316 sheet: -4.08 (0.63), residues: 27 loop : -1.94 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1839 TYR 0.046 0.002 TYR B1834 PHE 0.025 0.002 PHE B 802 TRP 0.004 0.001 TRP B1024 HIS 0.007 0.001 HIS B1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7163) covalent geometry : angle 0.69226 / 0.35 ( 9965) hydrogen bonds : bond 0.05429 / 6.11 ( 303) hydrogen bonds : angle 5.57681 / 6.43 ( 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 108 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 790 ARG cc_start: 0.2221 (mmt90) cc_final: 0.1820 (tmt170) REVERT: B 960 PHE cc_start: 0.4903 (OUTLIER) cc_final: 0.4399 (t80) REVERT: B 1038 CYS cc_start: 0.7166 (p) cc_final: 0.6805 (p) REVERT: B 1380 TRP cc_start: 0.3019 (OUTLIER) cc_final: 0.1252 (t60) REVERT: B 1813 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6914 (mt-10) outliers start: 25 outliers final: 15 residues processed: 100 average time/residue: 0.1013 time to fit residues: 13.3161 Evaluate side-chains 99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1315 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1346 MET 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: 0.6980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 6 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.172555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.156011 restraints weight = 18827.576| |-----------------------------------------------------------------------------| r_work (start): 0.4674 rms_B_bonded: 3.16 r_work: 0.4557 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7163 Z= 0.158 Angle : 0.690 10.689 9965 Z= 0.355 Chirality : 0.041 0.175 1153 Planarity : 0.006 0.067 1074 Dihedral : 18.218 173.376 1611 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.77 % Allowed : 22.92 % Favored : 73.31 % 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: -1.64 (0.31), residues: 702 helix: 0.08 (0.28), residues: 315 sheet: -3.88 (0.65), residues: 27 loop : -1.97 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1839 TYR 0.046 0.002 TYR B1834 PHE 0.053 0.002 PHE B1582 TRP 0.005 0.001 TRP B1024 HIS 0.007 0.001 HIS B1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 7163) covalent geometry : angle 0.68996 / 0.36 ( 9965) hydrogen bonds : bond 0.05397 / 6.05 ( 303) hydrogen bonds : angle 5.58155 / 6.51 ( 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 104 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: B 790 ARG cc_start: 0.2441 (mmt90) cc_final: 0.2048 (tmt170) REVERT: B 837 MET cc_start: 0.4473 (OUTLIER) cc_final: 0.4154 (tpt) REVERT: B 906 ARG cc_start: 0.4546 (tpp80) cc_final: 0.4013 (tpp-160) REVERT: B 935 ARG cc_start: 0.3669 (OUTLIER) cc_final: 0.3352 (tpp-160) REVERT: B 960 PHE cc_start: 0.4879 (OUTLIER) cc_final: 0.4432 (t80) REVERT: B 1038 CYS cc_start: 0.7147 (p) cc_final: 0.6770 (p) REVERT: B 1380 TRP cc_start: 0.2903 (OUTLIER) cc_final: 0.1102 (t60) REVERT: B 1813 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6740 (mt-10) outliers start: 24 outliers final: 17 residues processed: 97 average time/residue: 0.0855 time to fit residues: 10.9564 Evaluate side-chains 101 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 783 ASP Chi-restraints excluded: chain B residue 837 MET 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 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 1315 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1346 MET 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 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 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: 0.0020 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 63 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 overall best weight: 0.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.175299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.159196 restraints weight = 18876.517| |-----------------------------------------------------------------------------| r_work (start): 0.4738 rms_B_bonded: 3.15 r_work: 0.4624 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7163 Z= 0.143 Angle : 0.683 12.042 9965 Z= 0.350 Chirality : 0.040 0.181 1153 Planarity : 0.006 0.065 1074 Dihedral : 18.164 176.046 1611 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.41 % Favored : 92.45 % Rotamer: Outliers : 3.61 % Allowed : 23.70 % 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: -1.56 (0.31), residues: 702 helix: 0.18 (0.29), residues: 315 sheet: -3.79 (0.66), residues: 27 loop : -1.97 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1839 TYR 0.038 0.002 TYR B1834 PHE 0.036 0.002 PHE B1582 TRP 0.006 0.001 TRP B1024 HIS 0.005 0.001 HIS B1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7163) covalent geometry : angle 0.68309 / 0.35 ( 9965) hydrogen bonds : bond 0.05232 / 5.85 ( 303) hydrogen bonds : angle 5.40436 / 6.30 ( 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 106 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 790 ARG cc_start: 0.1824 (mmt90) cc_final: 0.1582 (tmt170) REVERT: B 906 ARG cc_start: 0.4506 (tpp80) cc_final: 0.4206 (tpp-160) REVERT: B 944 ARG cc_start: 0.4259 (ptp-170) cc_final: 0.3603 (ptp-170) REVERT: B 960 PHE cc_start: 0.4820 (OUTLIER) cc_final: 0.4388 (t80) REVERT: B 1038 CYS cc_start: 0.7013 (p) cc_final: 0.6658 (p) REVERT: B 1380 TRP cc_start: 0.2897 (OUTLIER) cc_final: 0.1244 (t60) REVERT: B 1898 ARG cc_start: 0.4747 (tpp-160) cc_final: 0.4529 (tpp-160) outliers start: 23 outliers final: 13 residues processed: 98 average time/residue: 0.0813 time to fit residues: 10.2939 Evaluate side-chains 98 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1037 LEU Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1346 MET 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 1810 ASP Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 39 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.173363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.157095 restraints weight = 18700.055| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 3.12 r_work: 0.4565 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.2706 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= 0.162 Angle : 0.705 11.235 9965 Z= 0.360 Chirality : 0.041 0.153 1153 Planarity : 0.006 0.069 1074 Dihedral : 18.129 175.472 1611 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.83 % Favored : 92.02 % Rotamer: Outliers : 2.67 % Allowed : 24.02 % Favored : 73.31 % 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: -1.64 (0.31), residues: 702 helix: 0.15 (0.29), residues: 314 sheet: -3.97 (0.61), residues: 37 loop : -1.95 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1839 TYR 0.046 0.002 TYR B1834 PHE 0.029 0.002 PHE B 896 TRP 0.004 0.001 TRP B1024 HIS 0.007 0.001 HIS B1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 7163) covalent geometry : angle 0.70499 / 0.36 ( 9965) hydrogen bonds : bond 0.05260 / 5.93 ( 303) hydrogen bonds : angle 5.52205 / 6.33 ( 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 104 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 790 ARG cc_start: 0.2261 (mmt90) cc_final: 0.1955 (tmt170) REVERT: B 960 PHE cc_start: 0.4819 (OUTLIER) cc_final: 0.4317 (t80) REVERT: B 1038 CYS cc_start: 0.7049 (p) cc_final: 0.6660 (p) REVERT: B 1380 TRP cc_start: 0.2954 (OUTLIER) cc_final: 0.1168 (t60) REVERT: B 1570 TYR cc_start: 0.3514 (p90) cc_final: 0.2646 (p90) REVERT: B 1898 ARG cc_start: 0.4549 (tpp-160) cc_final: 0.4269 (tpp-160) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 0.0898 time to fit residues: 11.2909 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 : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1037 LEU Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1346 MET 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 1577 ARG Chi-restraints excluded: chain B residue 1810 ASP Chi-restraints excluded: chain B residue 1849 VAL Chi-restraints excluded: chain B residue 1878 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.0040 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.0040 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.175546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.159267 restraints weight = 18660.314| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 3.14 r_work: 0.4596 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7163 Z= 0.147 Angle : 0.709 13.353 9965 Z= 0.361 Chirality : 0.040 0.160 1153 Planarity : 0.006 0.067 1074 Dihedral : 18.120 176.262 1611 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.41 % Favored : 92.45 % Rotamer: Outliers : 2.20 % Allowed : 24.80 % 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: -1.60 (0.31), residues: 702 helix: 0.26 (0.29), residues: 314 sheet: -3.87 (0.54), residues: 44 loop : -1.95 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 906 TYR 0.046 0.002 TYR B1834 PHE 0.039 0.002 PHE B1582 TRP 0.004 0.001 TRP B1024 HIS 0.007 0.001 HIS B1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7163) covalent geometry : angle 0.70931 / 0.36 ( 9965) hydrogen bonds : bond 0.05279 / 5.87 ( 303) hydrogen bonds : angle 5.40393 / 6.23 ( 821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.07 seconds wall clock time: 28 minutes 44.12 seconds (1724.12 seconds total)