Starting phenix.real_space_refine on Fri Sep 11 18:56:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w6o_65698/09_2026/9w6o_65698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w6o_65698/09_2026/9w6o_65698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w6o_65698/09_2026/9w6o_65698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w6o_65698/09_2026/9w6o_65698.map" model { file = "/net/cci-nas-00/data/ceres_data/9w6o_65698/09_2026/9w6o_65698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w6o_65698/09_2026/9w6o_65698.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 256 5.49 5 S 14 5.16 5 C 6026 2.51 5 N 2022 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10846 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 683 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "D" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 691 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 727 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2639 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain: "J" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2609 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Time building chain proxies: 2.57, per 1000 atoms: 0.24 Number of scatterers: 10846 At special positions: 0 Unit cell: (117.7, 89.1, 121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 256 15.00 O 2528 8.00 N 2022 7.00 C 6026 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: 0.94 Conformation dependent library (CDL) restraints added in 191.6 milliseconds 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 73.5% alpha, 0.6% beta 127 base pairs and 173 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.140A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.594A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.773A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.118A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 48 through 77 removed outlier: 4.475A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.382A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 4.651A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'D' and resid 37 through 48 Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.558A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.060A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 45 through 57 removed outlier: 4.483A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.039A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.633A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.714A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.785A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.941A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.313A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 39 through 49 removed outlier: 3.623A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 101 removed outlier: 3.816A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 122 Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.790A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.530A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 368 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 658 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 173 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1812 1.33 - 1.45: 3923 1.45 - 1.57: 5293 1.57 - 1.69: 510 1.69 - 1.81: 24 Bond restraints: 11562 Sorted by residual: bond pdb=" C3' DA I -1 " pdb=" C2' DA I -1 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DG I 32 " pdb=" C2' DG I 32 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG J -30 " pdb=" C2' DG J -30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.87e+00 ... (remaining 11557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 15168 1.13 - 2.26: 1318 2.26 - 3.39: 218 3.39 - 4.52: 6 4.52 - 5.65: 7 Bond angle restraints: 16717 Sorted by residual: angle pdb=" O4' DA I 42 " pdb=" C4' DA I 42 " pdb=" C3' DA I 42 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I -32 " pdb=" C4 DT I -32 " pdb=" O4 DT I -32 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 16712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4469 17.90 - 35.80: 834 35.80 - 53.71: 733 53.71 - 71.61: 208 71.61 - 89.51: 18 Dihedral angle restraints: 6262 sinusoidal: 4221 harmonic: 2041 Sorted by residual: dihedral pdb=" N GLN E 93 " pdb=" CA GLN E 93 " pdb=" CB GLN E 93 " pdb=" CG GLN E 93 " ideal model delta sinusoidal sigma weight residual -60.00 -108.80 48.80 3 1.50e+01 4.44e-03 8.69e+00 dihedral pdb=" N ARG F 36 " pdb=" CA ARG F 36 " pdb=" CB ARG F 36 " pdb=" CG ARG F 36 " ideal model delta sinusoidal sigma weight residual -60.00 -106.94 46.94 3 1.50e+01 4.44e-03 8.42e+00 dihedral pdb=" CB MET E 90 " pdb=" CG MET E 90 " pdb=" SD MET E 90 " pdb=" CE MET E 90 " ideal model delta sinusoidal sigma weight residual 60.00 104.16 -44.16 3 1.50e+01 4.44e-03 7.94e+00 ... (remaining 6259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1178 0.035 - 0.070: 531 0.070 - 0.105: 178 0.105 - 0.140: 18 0.140 - 0.176: 1 Chirality restraints: 1906 Sorted by residual: chirality pdb=" CA PHE C 25 " pdb=" N PHE C 25 " pdb=" C PHE C 25 " pdb=" CB PHE C 25 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA VAL F 43 " pdb=" N VAL F 43 " pdb=" C VAL F 43 " pdb=" CB VAL F 43 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1903 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO H 103 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 49 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO D 50 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -32 " -0.008 2.00e-02 2.50e+03 8.21e-03 1.52e+00 pdb=" N1 DC J -32 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DC J -32 " 0.019 2.00e-02 2.50e+03 pdb=" O2 DC J -32 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC J -32 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DC J -32 " -0.000 2.00e-02 2.50e+03 pdb=" N4 DC J -32 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DC J -32 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC J -32 " -0.002 2.00e-02 2.50e+03 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1697 2.77 - 3.30: 10108 3.30 - 3.83: 21060 3.83 - 4.37: 22413 4.37 - 4.90: 33092 Nonbonded interactions: 88370 Sorted by model distance: nonbonded pdb=" O2 DC J -32 " pdb=" N6 DA J -31 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.304 3.040 nonbonded pdb=" O LEU G 85 " pdb=" ND2 ASN G 89 " model vdw 2.311 3.120 nonbonded pdb=" O MET H 59 " pdb=" ND2 ASN H 63 " model vdw 2.321 3.120 ... (remaining 88365 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 24 through 111) } ncs_group { reference = (chain 'D' and resid 36 through 122) selection = (chain 'H' and resid 36 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.340 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 0.035 11562 Z= 0.505 Angle : 0.663 5.653 16717 Z= 0.626 Chirality : 0.041 0.176 1906 Planarity : 0.003 0.042 1227 Dihedral : 25.024 89.509 4948 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % 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: 3.00 (0.33), residues: 689 helix: 2.69 (0.24), residues: 489 sheet: None (None), residues: 0 loop : 0.21 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 71 TYR 0.005 0.001 TYR D 42 PHE 0.005 0.000 PHE C 25 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.50 (11562) covalent geometry : angle 0.66340 / 0.63 (16717) hydrogen bonds : bond 0.08225 / 5.53 ( 697) hydrogen bonds : angle 2.78233 / 2.01 ( 1750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6915 (ppp) cc_final: 0.5556 (tmm) REVERT: A 94 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 109 LEU cc_start: 0.8625 (mt) cc_final: 0.8396 (mt) REVERT: A 119 ILE cc_start: 0.8302 (mm) cc_final: 0.7900 (mm) REVERT: A 120 MET cc_start: 0.8132 (mmt) cc_final: 0.7803 (mmt) REVERT: B 26 ILE cc_start: 0.8553 (tp) cc_final: 0.8129 (tt) REVERT: C 57 TYR cc_start: 0.8327 (t80) cc_final: 0.7801 (t80) REVERT: D 71 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8416 (tp30) REVERT: D 85 LYS cc_start: 0.8547 (mmtt) cc_final: 0.7942 (mptt) REVERT: D 108 LYS cc_start: 0.8481 (pptt) cc_final: 0.8240 (pttp) REVERT: E 49 ARG cc_start: 0.8522 (ptp-170) cc_final: 0.8109 (ptp-110) REVERT: E 67 PHE cc_start: 0.8856 (t80) cc_final: 0.8461 (t80) REVERT: E 68 GLN cc_start: 0.8562 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 73 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7697 (mm-30) REVERT: E 84 PHE cc_start: 0.8861 (m-80) cc_final: 0.8183 (m-10) REVERT: E 86 SER cc_start: 0.8297 (t) cc_final: 0.8079 (m) REVERT: E 93 GLN cc_start: 0.8672 (mt0) cc_final: 0.8374 (mt0) REVERT: E 94 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7816 (mt-10) REVERT: E 96 CYS cc_start: 0.7929 (p) cc_final: 0.7396 (p) REVERT: F 32 PRO cc_start: 0.7784 (Cg_exo) cc_final: 0.7571 (Cg_endo) REVERT: F 43 VAL cc_start: 0.7805 (p) cc_final: 0.7507 (p) REVERT: F 53 GLU cc_start: 0.7627 (pt0) cc_final: 0.7417 (pt0) REVERT: F 80 THR cc_start: 0.7752 (m) cc_final: 0.7509 (p) REVERT: F 84 MET cc_start: 0.8204 (ppp) cc_final: 0.7148 (ppp) REVERT: F 97 LEU cc_start: 0.8911 (mm) cc_final: 0.8659 (mm) REVERT: G 57 TYR cc_start: 0.7968 (t80) cc_final: 0.7436 (t80) REVERT: H 76 GLU cc_start: 0.8655 (tp30) cc_final: 0.8431 (tp30) REVERT: H 90 THR cc_start: 0.7689 (p) cc_final: 0.6808 (p) REVERT: H 93 GLU cc_start: 0.8475 (mp0) cc_final: 0.8039 (mp0) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1529 time to fit residues: 60.5997 Evaluate side-chains 215 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.086881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073738 restraints weight = 58113.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.074985 restraints weight = 35438.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.075881 restraints weight = 24881.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.076493 restraints weight = 19211.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.076927 restraints weight = 15980.767| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11562 Z= 0.199 Angle : 0.634 5.644 16717 Z= 0.386 Chirality : 0.042 0.273 1906 Planarity : 0.005 0.054 1227 Dihedral : 29.198 89.579 3561 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: 2.23 (0.32), residues: 689 helix: 2.19 (0.23), residues: 490 sheet: None (None), residues: 0 loop : -0.33 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG F 36 TYR 0.017 0.002 TYR C 57 PHE 0.014 0.002 PHE E 104 HIS 0.008 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.20 (11562) covalent geometry : angle 0.63444 / 0.39 (16717) hydrogen bonds : bond 0.06179 / 4.20 ( 697) hydrogen bonds : angle 2.89989 / 2.11 ( 1750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9105 (tp) cc_final: 0.8796 (tp) REVERT: A 90 MET cc_start: 0.6779 (ppp) cc_final: 0.5193 (tmm) REVERT: A 94 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 26 ILE cc_start: 0.8599 (tp) cc_final: 0.8155 (tt) REVERT: B 44 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8110 (mmmm) REVERT: B 62 LEU cc_start: 0.9242 (mm) cc_final: 0.8716 (mm) REVERT: D 83 TYR cc_start: 0.7658 (t80) cc_final: 0.7397 (t80) REVERT: D 85 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8028 (mptt) REVERT: E 94 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7629 (mt-10) REVERT: E 108 ASN cc_start: 0.8637 (t0) cc_final: 0.8365 (t0) REVERT: F 84 MET cc_start: 0.8187 (ppp) cc_final: 0.7309 (ppp) REVERT: F 97 LEU cc_start: 0.9009 (mm) cc_final: 0.8725 (mm) REVERT: H 90 THR cc_start: 0.8281 (p) cc_final: 0.7254 (p) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1146 time to fit residues: 39.6420 Evaluate side-chains 209 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 71 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 chunk 74 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.079638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.066915 restraints weight = 59044.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.068147 restraints weight = 34883.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.068990 restraints weight = 24011.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.069534 restraints weight = 18342.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.069949 restraints weight = 15342.514| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 11562 Z= 0.240 Angle : 0.714 9.374 16717 Z= 0.421 Chirality : 0.045 0.231 1906 Planarity : 0.007 0.103 1227 Dihedral : 29.773 89.590 3561 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: 1.58 (0.32), residues: 689 helix: 1.69 (0.23), residues: 493 sheet: None (None), residues: 0 loop : -0.55 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 36 TYR 0.033 0.003 TYR G 50 PHE 0.029 0.002 PHE C 25 HIS 0.009 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.24 (11562) covalent geometry : angle 0.71414 / 0.42 (16717) hydrogen bonds : bond 0.06824 / 4.58 ( 697) hydrogen bonds : angle 3.20334 / 2.34 ( 1750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 90 MET cc_start: 0.6828 (ppp) cc_final: 0.5522 (tmm) REVERT: A 94 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 26 ILE cc_start: 0.8708 (tp) cc_final: 0.8197 (tt) REVERT: B 49 LEU cc_start: 0.9089 (mm) cc_final: 0.8139 (tp) REVERT: B 62 LEU cc_start: 0.9389 (mm) cc_final: 0.8864 (mm) REVERT: C 95 LYS cc_start: 0.8624 (tppt) cc_final: 0.8167 (tppt) REVERT: D 85 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8090 (mptt) REVERT: D 88 THR cc_start: 0.7168 (m) cc_final: 0.6750 (t) REVERT: E 60 LEU cc_start: 0.8940 (pp) cc_final: 0.8625 (pp) REVERT: F 52 GLU cc_start: 0.8568 (mp0) cc_final: 0.8317 (pm20) REVERT: F 84 MET cc_start: 0.8289 (ppp) cc_final: 0.7902 (ppp) REVERT: G 57 TYR cc_start: 0.8216 (t80) cc_final: 0.7496 (t80) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1298 time to fit residues: 44.9036 Evaluate side-chains 213 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.077746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064773 restraints weight = 59418.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.066038 restraints weight = 34892.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066893 restraints weight = 23950.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.067436 restraints weight = 18339.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.067846 restraints weight = 15378.477| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11562 Z= 0.193 Angle : 0.642 7.234 16717 Z= 0.387 Chirality : 0.041 0.177 1906 Planarity : 0.006 0.080 1227 Dihedral : 30.022 89.536 3561 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.34 % Allowed : 3.90 % Favored : 95.76 % 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: 1.77 (0.32), residues: 689 helix: 1.84 (0.23), residues: 495 sheet: None (None), residues: 0 loop : -0.54 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 78 TYR 0.021 0.002 TYR F 98 PHE 0.008 0.001 PHE A 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (11562) covalent geometry : angle 0.64235 / 0.39 (16717) hydrogen bonds : bond 0.05777 / 3.94 ( 697) hydrogen bonds : angle 3.10534 / 2.27 ( 1750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 90 MET cc_start: 0.7226 (ppp) cc_final: 0.5696 (tmm) REVERT: A 94 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 53 GLU cc_start: 0.8672 (mp0) cc_final: 0.7479 (mp0) REVERT: B 62 LEU cc_start: 0.9395 (mm) cc_final: 0.8953 (mm) REVERT: B 86 VAL cc_start: 0.9223 (t) cc_final: 0.9005 (p) REVERT: B 93 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8448 (mp10) REVERT: C 25 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: C 56 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8370 (mm-30) REVERT: C 57 TYR cc_start: 0.8671 (t80) cc_final: 0.7479 (t80) REVERT: C 95 LYS cc_start: 0.8353 (tppt) cc_final: 0.7887 (tppt) REVERT: D 85 LYS cc_start: 0.8606 (mmtt) cc_final: 0.7953 (mptt) REVERT: D 88 THR cc_start: 0.7628 (m) cc_final: 0.7338 (t) REVERT: E 108 ASN cc_start: 0.8965 (t160) cc_final: 0.8740 (t0) REVERT: F 53 GLU cc_start: 0.8144 (pt0) cc_final: 0.7813 (pt0) REVERT: F 84 MET cc_start: 0.8217 (ppp) cc_final: 0.7453 (ppp) REVERT: G 57 TYR cc_start: 0.8279 (t80) cc_final: 0.7614 (t80) REVERT: G 68 ASN cc_start: 0.7547 (m-40) cc_final: 0.6215 (m-40) REVERT: H 94 ILE cc_start: 0.9148 (pt) cc_final: 0.8824 (mt) outliers start: 2 outliers final: 0 residues processed: 253 average time/residue: 0.1185 time to fit residues: 40.4854 Evaluate side-chains 218 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 58 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 40.0000 chunk 2 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 76 optimal weight: 40.0000 chunk 35 optimal weight: 0.0570 chunk 16 optimal weight: 5.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.077646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.065038 restraints weight = 58895.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.066296 restraints weight = 34779.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.067155 restraints weight = 23837.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.067740 restraints weight = 18129.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068174 restraints weight = 14911.525| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11562 Z= 0.157 Angle : 0.602 6.387 16717 Z= 0.365 Chirality : 0.040 0.172 1906 Planarity : 0.005 0.070 1227 Dihedral : 30.097 89.973 3561 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 1.89 (0.32), residues: 689 helix: 2.00 (0.23), residues: 489 sheet: None (None), residues: 0 loop : -0.65 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 78 TYR 0.015 0.002 TYR B 51 PHE 0.022 0.002 PHE C 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.16 (11562) covalent geometry : angle 0.60237 / 0.36 (16717) hydrogen bonds : bond 0.05010 / 3.41 ( 697) hydrogen bonds : angle 2.94798 / 2.16 ( 1750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 90 MET cc_start: 0.7286 (ppp) cc_final: 0.5737 (tmm) REVERT: A 94 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 125 GLN cc_start: 0.8593 (mt0) cc_final: 0.8065 (mp10) REVERT: B 49 LEU cc_start: 0.8741 (mm) cc_final: 0.8412 (mm) REVERT: B 62 LEU cc_start: 0.9362 (mm) cc_final: 0.8942 (mm) REVERT: B 86 VAL cc_start: 0.9204 (t) cc_final: 0.8972 (p) REVERT: B 93 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8569 (mp10) REVERT: C 56 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8499 (mm-30) REVERT: C 95 LYS cc_start: 0.8395 (tppt) cc_final: 0.7909 (tppt) REVERT: D 85 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7893 (mptt) REVERT: D 88 THR cc_start: 0.7526 (m) cc_final: 0.7115 (t) REVERT: E 60 LEU cc_start: 0.9021 (pp) cc_final: 0.8648 (pp) REVERT: F 53 GLU cc_start: 0.7980 (pt0) cc_final: 0.7701 (pt0) REVERT: F 84 MET cc_start: 0.8251 (ppp) cc_final: 0.7635 (ppp) REVERT: G 57 TYR cc_start: 0.8230 (t80) cc_final: 0.7665 (t80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1212 time to fit residues: 41.3044 Evaluate side-chains 211 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 40.0000 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.077852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065075 restraints weight = 58319.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.066326 restraints weight = 33758.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.067203 restraints weight = 23026.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.067790 restraints weight = 17446.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.068161 restraints weight = 14402.815| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11562 Z= 0.149 Angle : 0.595 7.005 16717 Z= 0.359 Chirality : 0.039 0.170 1906 Planarity : 0.005 0.062 1227 Dihedral : 30.099 89.837 3561 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 1.89 (0.33), residues: 689 helix: 1.99 (0.24), residues: 494 sheet: None (None), residues: 0 loop : -0.69 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 29 TYR 0.023 0.002 TYR C 57 PHE 0.016 0.001 PHE C 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (11562) covalent geometry : angle 0.59465 / 0.36 (16717) hydrogen bonds : bond 0.04585 / 3.12 ( 697) hydrogen bonds : angle 2.89766 / 2.13 ( 1750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7229 (ppp) cc_final: 0.5642 (tmm) REVERT: A 94 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 125 GLN cc_start: 0.8594 (mt0) cc_final: 0.7995 (mp10) REVERT: B 49 LEU cc_start: 0.8559 (mm) cc_final: 0.8310 (mm) REVERT: B 59 LYS cc_start: 0.9240 (tmmt) cc_final: 0.8988 (tmtt) REVERT: B 62 LEU cc_start: 0.9385 (mm) cc_final: 0.9073 (mm) REVERT: B 86 VAL cc_start: 0.9190 (t) cc_final: 0.8966 (p) REVERT: C 57 TYR cc_start: 0.8417 (t80) cc_final: 0.7651 (t80) REVERT: C 95 LYS cc_start: 0.8405 (tppt) cc_final: 0.7904 (tppt) REVERT: D 85 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8155 (mmmt) REVERT: D 88 THR cc_start: 0.7261 (m) cc_final: 0.6839 (t) REVERT: F 84 MET cc_start: 0.8334 (ppp) cc_final: 0.7649 (ppp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1128 time to fit residues: 38.8539 Evaluate side-chains 216 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 40.0000 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.075780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063191 restraints weight = 59360.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064428 restraints weight = 34363.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.065290 restraints weight = 23328.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.065871 restraints weight = 17627.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.066228 restraints weight = 14586.558| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11562 Z= 0.179 Angle : 0.649 10.146 16717 Z= 0.380 Chirality : 0.040 0.199 1906 Planarity : 0.005 0.053 1227 Dihedral : 30.221 89.951 3561 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 1.76 (0.33), residues: 689 helix: 1.91 (0.24), residues: 494 sheet: None (None), residues: 0 loop : -0.79 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 78 TYR 0.038 0.002 TYR C 57 PHE 0.011 0.002 PHE A 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 (11562) covalent geometry : angle 0.64888 / 0.38 (16717) hydrogen bonds : bond 0.05442 / 3.70 ( 697) hydrogen bonds : angle 3.03297 / 2.22 ( 1750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7289 (ppp) cc_final: 0.5766 (tmm) REVERT: A 94 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7971 (mt-10) REVERT: B 59 LYS cc_start: 0.9295 (tmmt) cc_final: 0.9043 (tmtt) REVERT: B 62 LEU cc_start: 0.9458 (mm) cc_final: 0.9064 (mm) REVERT: B 78 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7910 (mtm-85) REVERT: B 93 GLN cc_start: 0.8528 (mp10) cc_final: 0.8254 (mp10) REVERT: C 95 LYS cc_start: 0.8452 (tppt) cc_final: 0.7909 (tppt) REVERT: D 85 LYS cc_start: 0.8562 (mmtt) cc_final: 0.7985 (mmtm) REVERT: D 88 THR cc_start: 0.7416 (m) cc_final: 0.6977 (t) REVERT: E 60 LEU cc_start: 0.8901 (pp) cc_final: 0.8627 (pp) REVERT: F 84 MET cc_start: 0.8346 (ppp) cc_final: 0.7706 (ppp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1128 time to fit residues: 37.6650 Evaluate side-chains 207 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.073606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061232 restraints weight = 60099.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.062358 restraints weight = 34692.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.063120 restraints weight = 23791.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063649 restraints weight = 18213.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063995 restraints weight = 15241.554| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11562 Z= 0.189 Angle : 0.667 9.033 16717 Z= 0.392 Chirality : 0.042 0.184 1906 Planarity : 0.005 0.051 1227 Dihedral : 30.439 89.937 3561 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 1.47 (0.32), residues: 689 helix: 1.68 (0.23), residues: 495 sheet: None (None), residues: 0 loop : -0.85 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 78 TYR 0.026 0.003 TYR B 51 PHE 0.013 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (11562) covalent geometry : angle 0.66731 / 0.39 (16717) hydrogen bonds : bond 0.05637 / 3.83 ( 697) hydrogen bonds : angle 3.17762 / 2.31 ( 1750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8287 (mm) cc_final: 0.7731 (mm) REVERT: A 90 MET cc_start: 0.7265 (ppp) cc_final: 0.5775 (tmm) REVERT: A 94 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7974 (mt-10) REVERT: B 49 LEU cc_start: 0.8890 (mm) cc_final: 0.8590 (mm) REVERT: B 58 LEU cc_start: 0.9423 (tp) cc_final: 0.9203 (tp) REVERT: B 62 LEU cc_start: 0.9491 (mm) cc_final: 0.9120 (mm) REVERT: C 95 LYS cc_start: 0.8599 (tppt) cc_final: 0.8021 (tppt) REVERT: D 85 LYS cc_start: 0.8518 (mmtt) cc_final: 0.7954 (mmtm) REVERT: D 88 THR cc_start: 0.7603 (m) cc_final: 0.7221 (t) REVERT: F 84 MET cc_start: 0.8325 (ppp) cc_final: 0.7719 (ppp) REVERT: G 68 ASN cc_start: 0.7490 (m110) cc_final: 0.7196 (m-40) REVERT: H 46 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8607 (mmtm) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1109 time to fit residues: 38.0862 Evaluate side-chains 205 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 83 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.073486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.061580 restraints weight = 61108.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062580 restraints weight = 37286.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.063298 restraints weight = 26419.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063806 restraints weight = 20742.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064147 restraints weight = 17556.357| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11562 Z= 0.163 Angle : 0.642 8.425 16717 Z= 0.383 Chirality : 0.040 0.182 1906 Planarity : 0.005 0.051 1227 Dihedral : 30.419 89.342 3561 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 689 helix: 1.68 (0.24), residues: 494 sheet: None (None), residues: 0 loop : -0.80 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 72 TYR 0.047 0.002 TYR G 57 PHE 0.013 0.001 PHE C 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (11562) covalent geometry : angle 0.64200 / 0.38 (16717) hydrogen bonds : bond 0.05060 / 3.43 ( 697) hydrogen bonds : angle 3.21680 / 2.33 ( 1750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 90 MET cc_start: 0.7086 (ppp) cc_final: 0.5540 (tmm) REVERT: A 94 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 49 LEU cc_start: 0.8747 (mm) cc_final: 0.8004 (mm) REVERT: B 53 GLU cc_start: 0.8359 (mp0) cc_final: 0.8030 (mp0) REVERT: B 59 LYS cc_start: 0.9171 (tmmt) cc_final: 0.8971 (tmtt) REVERT: B 62 LEU cc_start: 0.9421 (mm) cc_final: 0.9080 (mm) REVERT: C 95 LYS cc_start: 0.8336 (tppt) cc_final: 0.7823 (tppt) REVERT: D 46 LYS cc_start: 0.8650 (mmpt) cc_final: 0.7945 (mttp) REVERT: D 85 LYS cc_start: 0.8451 (mmtt) cc_final: 0.7911 (mmtm) REVERT: D 88 THR cc_start: 0.7587 (m) cc_final: 0.7110 (t) REVERT: F 70 VAL cc_start: 0.9263 (t) cc_final: 0.8952 (t) REVERT: F 84 MET cc_start: 0.8095 (ppp) cc_final: 0.7609 (ppp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1175 time to fit residues: 39.0975 Evaluate side-chains 207 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 40.0000 chunk 6 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.072808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060599 restraints weight = 59187.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.061764 restraints weight = 33376.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062567 restraints weight = 22554.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.063155 restraints weight = 17005.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063485 restraints weight = 14000.532| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11562 Z= 0.163 Angle : 0.660 8.983 16717 Z= 0.387 Chirality : 0.040 0.182 1906 Planarity : 0.005 0.055 1227 Dihedral : 30.421 89.894 3561 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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 (0.32), residues: 689 helix: 1.77 (0.24), residues: 492 sheet: None (None), residues: 0 loop : -0.83 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 79 TYR 0.020 0.002 TYR B 51 PHE 0.015 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (11562) covalent geometry : angle 0.66040 / 0.39 (16717) hydrogen bonds : bond 0.05009 / 3.38 ( 697) hydrogen bonds : angle 3.19141 / 2.30 ( 1750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 53 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7305 (ttp80) REVERT: A 90 MET cc_start: 0.7267 (ppp) cc_final: 0.5739 (tmm) REVERT: A 94 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 109 LEU cc_start: 0.8669 (mt) cc_final: 0.8457 (mt) REVERT: B 49 LEU cc_start: 0.8955 (mm) cc_final: 0.8451 (mm) REVERT: B 59 LYS cc_start: 0.9223 (tmmt) cc_final: 0.8980 (tmtt) REVERT: B 62 LEU cc_start: 0.9457 (mm) cc_final: 0.9145 (mm) REVERT: C 95 LYS cc_start: 0.8456 (tppt) cc_final: 0.7883 (tppt) REVERT: D 46 LYS cc_start: 0.8787 (mmpt) cc_final: 0.8083 (mttp) REVERT: D 85 LYS cc_start: 0.8457 (mmtt) cc_final: 0.7904 (mmtm) REVERT: D 88 THR cc_start: 0.7658 (m) cc_final: 0.7190 (t) REVERT: F 84 MET cc_start: 0.8382 (ppp) cc_final: 0.7654 (ppp) REVERT: G 68 ASN cc_start: 0.7686 (m-40) cc_final: 0.6597 (m110) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1192 time to fit residues: 39.0249 Evaluate side-chains 216 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 40.0000 chunk 69 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.071996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.059738 restraints weight = 59514.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060886 restraints weight = 33823.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.061691 restraints weight = 22962.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062194 restraints weight = 17397.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062511 restraints weight = 14473.291| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11562 Z= 0.176 Angle : 0.669 7.476 16717 Z= 0.394 Chirality : 0.041 0.187 1906 Planarity : 0.005 0.049 1227 Dihedral : 30.504 89.904 3561 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.17 % Allowed : 0.34 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.46 (0.32), residues: 689 helix: 1.69 (0.24), residues: 493 sheet: None (None), residues: 0 loop : -0.87 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 69 TYR 0.033 0.002 TYR E 54 PHE 0.015 0.002 PHE C 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (11562) covalent geometry : angle 0.66860 / 0.39 (16717) hydrogen bonds : bond 0.05411 / 3.66 ( 697) hydrogen bonds : angle 3.29541 / 2.38 ( 1750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1712.23 seconds wall clock time: 30 minutes 18.10 seconds (1818.10 seconds total)