Starting phenix.real_space_refine on Fri Sep 11 21:04:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g86_29837/09_2026/8g86_29837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g86_29837/09_2026/8g86_29837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g86_29837/09_2026/8g86_29837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g86_29837/09_2026/8g86_29837.map" model { file = "/net/cci-nas-00/data/ceres_data/8g86_29837/09_2026/8g86_29837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g86_29837/09_2026/8g86_29837.cif" } resolution = 2.3 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 290 5.49 5 S 12 5.16 5 C 6637 2.51 5 N 2229 2.21 5 O 2804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 11972 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2995 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11972 At special positions: 0 Unit cell: (74.865, 116.725, 114.31, 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 12 16.00 P 290 15.00 O 2804 8.00 N 2229 7.00 C 6637 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: 0.81 Conformation dependent library (CDL) restraints added in 356.5 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.4% alpha, 2.9% beta 134 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.145A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.236A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'E' and resid 44 through 55 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 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.829A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.387A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.003A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.691A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.769A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.764A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.057A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 417 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 319 hydrogen bonds 634 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2227 1.33 - 1.45: 4184 1.45 - 1.57: 5764 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12775 Sorted by residual: bond pdb=" C3' DT J 41 " pdb=" C2' DT J 41 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC I -22 " pdb=" C2' DC I -22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DG I 68 " pdb=" C2' DG I 68 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA I -31 " pdb=" C2' DA I -31 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT J -11 " pdb=" C2' DT J -11 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 12770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 17359 1.41 - 2.83: 1105 2.83 - 4.24: 25 4.24 - 5.65: 6 5.65 - 7.06: 3 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N3 DT J -63 " pdb=" C4 DT J -63 " pdb=" O4 DT J -63 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT I -71 " pdb=" C4 DT I -71 " pdb=" O4 DT I -71 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT J 64 " pdb=" C4 DT J 64 " pdb=" O4 DT J 64 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT J 25 " pdb=" C4 DT J 25 " pdb=" O4 DT J 25 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT J 58 " pdb=" C4 DT J 58 " pdb=" O4 DT J 58 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 18493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 5664 35.88 - 71.77: 1344 71.77 - 107.65: 13 107.65 - 143.53: 0 143.53 - 179.41: 1 Dihedral angle restraints: 7022 sinusoidal: 4817 harmonic: 2205 Sorted by residual: dihedral pdb=" C4' DT I 20 " pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.41 -179.41 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU F 74 " pdb=" CG GLU F 74 " pdb=" CD GLU F 74 " pdb=" OE1 GLU F 74 " ideal model delta sinusoidal sigma weight residual 0.00 -88.78 88.78 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1042 0.026 - 0.052: 648 0.052 - 0.078: 203 0.078 - 0.104: 172 0.104 - 0.130: 44 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2106 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO G 80 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO C 80 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 66 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.019 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2611 2.81 - 3.33: 10262 3.33 - 3.85: 24101 3.85 - 4.38: 30291 4.38 - 4.90: 40295 Nonbonded interactions: 107560 Sorted by model distance: nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG E 72 " pdb=" OP1 DT J -23 " model vdw 2.328 3.120 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DC I -42 " model vdw 2.386 3.120 nonbonded pdb=" O2 DC I -42 " pdb=" N2 DG J 42 " model vdw 2.395 3.120 nonbonded pdb=" O2 DC I -51 " pdb=" N2 DG J 51 " model vdw 2.425 2.496 ... (remaining 107555 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 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 4.100 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.250 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.006 0.033 12775 Z= 0.515 Angle : 0.683 7.065 18498 Z= 0.628 Chirality : 0.043 0.130 2109 Planarity : 0.003 0.047 1335 Dihedral : 27.264 179.413 5598 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.95 % Allowed : 16.30 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.28), residues: 743 helix: 1.47 (0.20), residues: 551 sheet: None (None), residues: 0 loop : 0.04 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.010 0.001 TYR B 51 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.51 (12775) covalent geometry : angle 0.68340 / 0.63 (18498) hydrogen bonds : bond 0.23805 / 16.33 ( 736) hydrogen bonds : angle 8.65357 / 6.37 ( 1861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.319 Fit side-chains REVERT: A 40 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7789 (mtp85) REVERT: A 120 MET cc_start: 0.8545 (mtt) cc_final: 0.8326 (mtp) REVERT: B 79 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8096 (mtmm) REVERT: C 110 ASN cc_start: 0.8575 (t0) cc_final: 0.8350 (t0) REVERT: D 73 GLU cc_start: 0.8617 (tp30) cc_final: 0.8383 (tp30) REVERT: D 113 LYS cc_start: 0.8106 (ttmp) cc_final: 0.7757 (ttpp) REVERT: E 59 GLU cc_start: 0.8053 (pm20) cc_final: 0.7843 (pm20) REVERT: F 27 GLN cc_start: 0.8276 (mm110) cc_final: 0.7981 (mm110) REVERT: G 15 LYS cc_start: 0.7400 (mtpt) cc_final: 0.6750 (tttt) REVERT: G 71 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6668 (ttm-80) REVERT: G 75 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7803 (mmtp) REVERT: H 54 LYS cc_start: 0.8614 (tptt) cc_final: 0.8385 (mmmm) outliers start: 6 outliers final: 2 residues processed: 163 average time/residue: 0.9210 time to fit residues: 158.0009 Evaluate side-chains 142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 44 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.177323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134367 restraints weight = 10875.910| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 0.92 r_work: 0.3365 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12775 Z= 0.193 Angle : 0.744 9.906 18498 Z= 0.421 Chirality : 0.050 0.222 2109 Planarity : 0.005 0.040 1335 Dihedral : 30.335 177.588 4097 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.64 % Allowed : 16.14 % Favored : 80.22 % 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: 2.45 (0.29), residues: 743 helix: 2.18 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.06 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.014 0.002 TYR B 51 PHE 0.014 0.002 PHE A 67 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (12775) covalent geometry : angle 0.74423 / 0.42 (18498) hydrogen bonds : bond 0.07171 / 4.86 ( 736) hydrogen bonds : angle 3.35064 / 2.39 ( 1861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.320 Fit side-chains REVERT: A 120 MET cc_start: 0.8393 (mtt) cc_final: 0.8173 (mtp) REVERT: A 131 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7479 (mtp180) REVERT: B 79 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8389 (mtmm) REVERT: C 110 ASN cc_start: 0.8683 (t0) cc_final: 0.8360 (t0) REVERT: D 105 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7887 (ttmt) REVERT: D 113 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7907 (tttm) REVERT: E 59 GLU cc_start: 0.8303 (pm20) cc_final: 0.8061 (pm20) REVERT: F 27 GLN cc_start: 0.8535 (mm110) cc_final: 0.8184 (mm110) REVERT: F 77 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8146 (mtpt) REVERT: G 15 LYS cc_start: 0.7474 (mtpt) cc_final: 0.6816 (tttt) REVERT: G 71 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6916 (ttm-80) REVERT: G 75 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7952 (mmtt) REVERT: H 105 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7486 (mmtt) outliers start: 23 outliers final: 9 residues processed: 157 average time/residue: 0.9505 time to fit residues: 156.7851 Evaluate side-chains 157 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.174832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133014 restraints weight = 10639.656| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 0.91 r_work: 0.3353 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12775 Z= 0.209 Angle : 0.730 7.866 18498 Z= 0.406 Chirality : 0.049 0.236 2109 Planarity : 0.005 0.042 1335 Dihedral : 31.042 177.805 4097 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.96 % Allowed : 15.66 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.29), residues: 743 helix: 2.14 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.19 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.016 0.002 TYR G 57 PHE 0.014 0.002 PHE A 67 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (12775) covalent geometry : angle 0.72982 / 0.41 (18498) hydrogen bonds : bond 0.07775 / 5.29 ( 736) hydrogen bonds : angle 3.26895 / 2.33 ( 1861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.320 Fit side-chains REVERT: A 120 MET cc_start: 0.8540 (mtt) cc_final: 0.8338 (mtp) REVERT: A 131 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7542 (mtp180) REVERT: B 79 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8441 (mtmm) REVERT: C 36 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8270 (mmpt) REVERT: C 110 ASN cc_start: 0.8724 (t0) cc_final: 0.8366 (t0) REVERT: D 105 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7990 (mtpt) REVERT: D 113 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8001 (tttm) REVERT: F 27 GLN cc_start: 0.8566 (mm110) cc_final: 0.8193 (mm110) REVERT: F 77 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8191 (mtpt) REVERT: G 15 LYS cc_start: 0.7604 (mtpt) cc_final: 0.6930 (tttt) REVERT: G 71 ARG cc_start: 0.7495 (ttp-110) cc_final: 0.7002 (ttm-80) REVERT: G 75 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8240 (mmtm) REVERT: G 95 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8432 (tmtm) REVERT: H 105 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7606 (mmtt) outliers start: 25 outliers final: 9 residues processed: 162 average time/residue: 0.9709 time to fit residues: 165.2649 Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 30.0000 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.176472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134889 restraints weight = 10626.187| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 0.90 r_work: 0.3379 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12775 Z= 0.157 Angle : 0.663 7.301 18498 Z= 0.377 Chirality : 0.045 0.237 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.994 179.487 4097 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.32 % Allowed : 15.82 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.29), residues: 743 helix: 2.32 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.011 0.002 TYR F 51 PHE 0.014 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (12775) covalent geometry : angle 0.66266 / 0.38 (18498) hydrogen bonds : bond 0.06210 / 4.18 ( 736) hydrogen bonds : angle 3.12512 / 2.22 ( 1861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.292 Fit side-chains REVERT: A 59 GLU cc_start: 0.8442 (pm20) cc_final: 0.8236 (pm20) REVERT: A 120 MET cc_start: 0.8465 (mtt) cc_final: 0.8255 (mtp) REVERT: A 131 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7559 (mtp180) REVERT: B 79 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8454 (mtmm) REVERT: C 36 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8220 (mmpt) REVERT: C 110 ASN cc_start: 0.8714 (t0) cc_final: 0.8358 (t0) REVERT: D 82 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8276 (mtmm) REVERT: D 105 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7910 (mtpt) REVERT: D 113 LYS cc_start: 0.8547 (ttmp) cc_final: 0.7986 (tttm) REVERT: F 27 GLN cc_start: 0.8557 (mm110) cc_final: 0.8172 (mm110) REVERT: F 77 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8168 (mtpt) REVERT: F 93 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: G 15 LYS cc_start: 0.7591 (mtpt) cc_final: 0.6919 (tttt) REVERT: G 71 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.6988 (ttm-80) REVERT: G 75 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8230 (mmtm) REVERT: G 95 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8406 (tmtm) REVERT: H 105 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7535 (mmtt) outliers start: 21 outliers final: 10 residues processed: 156 average time/residue: 0.9374 time to fit residues: 153.9653 Evaluate side-chains 159 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.0770 chunk 2 optimal weight: 0.0470 chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 24 GLN C 104 GLN D 44 GLN E 68 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135527 restraints weight = 10642.334| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 0.91 r_work: 0.3387 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12775 Z= 0.143 Angle : 0.647 7.574 18498 Z= 0.369 Chirality : 0.043 0.233 2109 Planarity : 0.004 0.039 1335 Dihedral : 30.949 179.715 4097 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.53 % Allowed : 16.93 % Favored : 80.54 % 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: 2.70 (0.29), residues: 743 helix: 2.42 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.012 0.001 TYR B 51 PHE 0.013 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (12775) covalent geometry : angle 0.64695 / 0.37 (18498) hydrogen bonds : bond 0.05826 / 3.91 ( 736) hydrogen bonds : angle 3.10794 / 2.21 ( 1861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.357 Fit side-chains REVERT: A 120 MET cc_start: 0.8448 (mtt) cc_final: 0.8234 (mtp) REVERT: A 131 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7560 (mtp180) REVERT: B 79 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8447 (mtmm) REVERT: C 36 LYS cc_start: 0.8537 (mmtm) cc_final: 0.8248 (mmpt) REVERT: C 110 ASN cc_start: 0.8718 (t0) cc_final: 0.8355 (t0) REVERT: D 82 LYS cc_start: 0.8612 (mmtp) cc_final: 0.8259 (mtmm) REVERT: D 113 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7980 (tttm) REVERT: F 27 GLN cc_start: 0.8561 (mm110) cc_final: 0.8167 (mm110) REVERT: F 77 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8173 (mtpt) REVERT: F 93 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: G 15 LYS cc_start: 0.7641 (mtpt) cc_final: 0.6944 (tttt) REVERT: G 71 ARG cc_start: 0.7506 (ttp-110) cc_final: 0.7135 (ttm110) REVERT: H 105 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7506 (mmtt) outliers start: 16 outliers final: 8 residues processed: 147 average time/residue: 0.9521 time to fit residues: 147.3130 Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 99 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 87 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 68 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132875 restraints weight = 10630.072| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.91 r_work: 0.3356 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12775 Z= 0.198 Angle : 0.708 8.104 18498 Z= 0.394 Chirality : 0.048 0.245 2109 Planarity : 0.005 0.044 1335 Dihedral : 31.140 176.775 4096 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.85 % Allowed : 16.14 % Favored : 81.01 % 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: 2.42 (0.29), residues: 743 helix: 2.21 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.26 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 92 TYR 0.013 0.002 TYR E 54 PHE 0.013 0.002 PHE A 67 HIS 0.005 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (12775) covalent geometry : angle 0.70799 / 0.39 (18498) hydrogen bonds : bond 0.07312 / 4.95 ( 736) hydrogen bonds : angle 3.18506 / 2.27 ( 1861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.282 Fit side-chains REVERT: A 59 GLU cc_start: 0.8526 (pm20) cc_final: 0.8315 (pm20) REVERT: A 120 MET cc_start: 0.8521 (mtt) cc_final: 0.8307 (mtp) REVERT: A 131 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7525 (mtp180) REVERT: B 79 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8440 (mtmm) REVERT: C 36 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8217 (mmpt) REVERT: C 92 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8063 (mt-10) REVERT: D 73 GLU cc_start: 0.8639 (tp30) cc_final: 0.8311 (tp30) REVERT: D 113 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8005 (tttm) REVERT: F 27 GLN cc_start: 0.8618 (mm110) cc_final: 0.8298 (mm110) REVERT: F 77 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8158 (mtpt) REVERT: F 93 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: G 15 LYS cc_start: 0.7705 (mtpt) cc_final: 0.6963 (tttt) REVERT: G 71 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7056 (ttm-80) REVERT: G 75 LYS cc_start: 0.8625 (mmtm) cc_final: 0.8418 (mmtt) REVERT: G 95 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8403 (tmtm) REVERT: H 105 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7603 (mmtt) outliers start: 18 outliers final: 8 residues processed: 153 average time/residue: 0.9470 time to fit residues: 152.4396 Evaluate side-chains 157 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 68 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133371 restraints weight = 10712.197| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.91 r_work: 0.3350 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12775 Z= 0.143 Angle : 0.663 7.564 18498 Z= 0.374 Chirality : 0.044 0.226 2109 Planarity : 0.004 0.039 1335 Dihedral : 31.117 177.368 4096 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.53 % Allowed : 16.61 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.29), residues: 743 helix: 2.38 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 92 TYR 0.012 0.002 TYR H 80 PHE 0.012 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (12775) covalent geometry : angle 0.66302 / 0.37 (18498) hydrogen bonds : bond 0.05953 / 3.99 ( 736) hydrogen bonds : angle 3.15450 / 2.25 ( 1861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.324 Fit side-chains REVERT: A 59 GLU cc_start: 0.8464 (pm20) cc_final: 0.8263 (pm20) REVERT: A 120 MET cc_start: 0.8510 (mtt) cc_final: 0.8292 (mtp) REVERT: A 131 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7527 (mtp180) REVERT: B 79 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8425 (mtmm) REVERT: C 36 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8199 (mmpt) REVERT: C 92 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8030 (mt-10) REVERT: D 82 LYS cc_start: 0.8635 (mmtp) cc_final: 0.8302 (mtmm) REVERT: D 113 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7985 (tttm) REVERT: F 27 GLN cc_start: 0.8599 (mm110) cc_final: 0.8276 (mm110) REVERT: F 77 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8114 (mtpt) REVERT: F 93 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: G 15 LYS cc_start: 0.7708 (mtpt) cc_final: 0.6968 (tttt) REVERT: G 71 ARG cc_start: 0.7622 (ttp-110) cc_final: 0.7062 (ttm-80) REVERT: G 75 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8377 (mmtt) REVERT: G 95 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8391 (tmtm) REVERT: H 105 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7572 (mmtt) outliers start: 16 outliers final: 7 residues processed: 153 average time/residue: 0.9483 time to fit residues: 152.7202 Evaluate side-chains 157 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 40.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 68 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132350 restraints weight = 10715.395| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 0.90 r_work: 0.3337 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12775 Z= 0.183 Angle : 0.674 7.890 18498 Z= 0.380 Chirality : 0.046 0.250 2109 Planarity : 0.005 0.043 1335 Dihedral : 31.120 178.283 4096 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.53 % Allowed : 17.09 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.29), residues: 743 helix: 2.31 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.24 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 92 TYR 0.012 0.002 TYR B 51 PHE 0.013 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (12775) covalent geometry : angle 0.67446 / 0.38 (18498) hydrogen bonds : bond 0.06535 / 4.39 ( 736) hydrogen bonds : angle 3.12021 / 2.22 ( 1861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.302 Fit side-chains REVERT: A 59 GLU cc_start: 0.8533 (pm20) cc_final: 0.8321 (pm20) REVERT: A 120 MET cc_start: 0.8531 (mtt) cc_final: 0.8314 (mtp) REVERT: A 131 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7524 (mtp180) REVERT: B 79 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8426 (mtmm) REVERT: C 92 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 73 GLU cc_start: 0.8628 (tp30) cc_final: 0.8310 (tp30) REVERT: D 82 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8315 (mtmm) REVERT: D 102 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7451 (mm-30) REVERT: D 113 LYS cc_start: 0.8620 (ttmp) cc_final: 0.8033 (tttm) REVERT: F 27 GLN cc_start: 0.8656 (mm110) cc_final: 0.8330 (mm110) REVERT: F 77 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8119 (mtpt) REVERT: F 93 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7857 (mt0) REVERT: G 15 LYS cc_start: 0.7711 (mtpt) cc_final: 0.6974 (tttt) REVERT: G 71 ARG cc_start: 0.7632 (ttp-110) cc_final: 0.7063 (ttm-80) REVERT: G 75 LYS cc_start: 0.8621 (mmtm) cc_final: 0.8419 (mmtt) REVERT: G 95 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8445 (tmtm) REVERT: H 105 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7583 (mmtt) outliers start: 16 outliers final: 8 residues processed: 152 average time/residue: 0.9182 time to fit residues: 146.9096 Evaluate side-chains 155 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 105 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 39 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 68 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134805 restraints weight = 10780.090| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 0.91 r_work: 0.3368 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12775 Z= 0.128 Angle : 0.635 7.618 18498 Z= 0.362 Chirality : 0.043 0.223 2109 Planarity : 0.004 0.039 1335 Dihedral : 31.074 178.571 4096 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.37 % Allowed : 17.56 % Favored : 80.06 % 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: 2.76 (0.29), residues: 743 helix: 2.47 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 20 TYR 0.011 0.001 TYR H 80 PHE 0.013 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.13 (12775) covalent geometry : angle 0.63520 / 0.36 (18498) hydrogen bonds : bond 0.05338 / 3.52 ( 736) hydrogen bonds : angle 3.09216 / 2.20 ( 1861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.313 Fit side-chains REVERT: A 59 GLU cc_start: 0.8497 (pm20) cc_final: 0.8281 (pm20) REVERT: A 120 MET cc_start: 0.8483 (mtt) cc_final: 0.8265 (mtp) REVERT: A 131 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7500 (mtp180) REVERT: B 79 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8423 (mtmm) REVERT: C 36 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8204 (mmpt) REVERT: C 92 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 82 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8288 (mtmm) REVERT: D 102 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7455 (mm-30) REVERT: D 113 LYS cc_start: 0.8568 (ttmp) cc_final: 0.7971 (tttm) REVERT: F 27 GLN cc_start: 0.8605 (mm110) cc_final: 0.8283 (mm110) REVERT: F 77 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8087 (mtpt) REVERT: F 93 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: G 15 LYS cc_start: 0.7709 (mtpt) cc_final: 0.6971 (tttt) REVERT: G 71 ARG cc_start: 0.7619 (ttp-110) cc_final: 0.7046 (ttm-80) REVERT: G 75 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8361 (mmtt) REVERT: G 95 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8411 (tmtm) REVERT: H 105 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7528 (mmtt) outliers start: 15 outliers final: 6 residues processed: 157 average time/residue: 0.9351 time to fit residues: 154.6358 Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN D 44 GLN E 68 GLN E 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134460 restraints weight = 10839.013| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 0.91 r_work: 0.3363 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12775 Z= 0.140 Angle : 0.621 7.449 18498 Z= 0.356 Chirality : 0.043 0.242 2109 Planarity : 0.004 0.072 1335 Dihedral : 30.969 179.868 4096 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.90 % Allowed : 18.51 % Favored : 79.59 % 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: 2.86 (0.29), residues: 743 helix: 2.54 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.14 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 20 TYR 0.013 0.002 TYR B 51 PHE 0.013 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12775) covalent geometry : angle 0.62108 / 0.36 (18498) hydrogen bonds : bond 0.05445 / 3.60 ( 736) hydrogen bonds : angle 3.00736 / 2.14 ( 1861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.319 Fit side-chains REVERT: A 59 GLU cc_start: 0.8501 (pm20) cc_final: 0.8222 (pm20) REVERT: A 120 MET cc_start: 0.8454 (mtt) cc_final: 0.8231 (mtp) REVERT: A 131 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7545 (mtp180) REVERT: B 79 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8415 (mtmm) REVERT: C 36 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8198 (mmpt) REVERT: C 92 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8039 (mt-10) REVERT: D 82 LYS cc_start: 0.8594 (mmtp) cc_final: 0.8283 (mtmm) REVERT: D 102 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7480 (mm-30) REVERT: D 113 LYS cc_start: 0.8575 (ttmp) cc_final: 0.8012 (tttm) REVERT: F 27 GLN cc_start: 0.8604 (mm110) cc_final: 0.8276 (mm110) REVERT: F 77 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8073 (mtpt) REVERT: G 15 LYS cc_start: 0.7720 (mtpt) cc_final: 0.6984 (tttt) REVERT: G 71 ARG cc_start: 0.7610 (ttp-110) cc_final: 0.7047 (ttm-80) REVERT: G 75 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8340 (mmtt) REVERT: G 95 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8388 (tmtm) REVERT: H 105 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7518 (mmtt) outliers start: 12 outliers final: 6 residues processed: 152 average time/residue: 0.9466 time to fit residues: 151.4881 Evaluate side-chains 154 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 75 HIS C 104 GLN D 44 GLN E 68 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.172783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129823 restraints weight = 10664.224| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 0.91 r_work: 0.3304 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 12775 Z= 0.279 Angle : 0.787 8.516 18498 Z= 0.428 Chirality : 0.054 0.271 2109 Planarity : 0.006 0.067 1335 Dihedral : 31.394 174.436 4096 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.22 % Allowed : 18.35 % Favored : 79.43 % 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: 2.16 (0.29), residues: 743 helix: 2.01 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.33 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.017 0.003 TYR E 54 PHE 0.018 0.003 PHE C 25 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.28 (12775) covalent geometry : angle 0.78734 / 0.43 (18498) hydrogen bonds : bond 0.08708 / 5.95 ( 736) hydrogen bonds : angle 3.32343 / 2.38 ( 1861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5315.50 seconds wall clock time: 90 minutes 53.59 seconds (5453.59 seconds total)