Starting phenix.real_space_refine on Sat Aug 23 11:03:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g86_29837/08_2025/8g86_29837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g86_29837/08_2025/8g86_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g86_29837/08_2025/8g86_29837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g86_29837/08_2025/8g86_29837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g86_29837/08_2025/8g86_29837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g86_29837/08_2025/8g86_29837.map" } 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-2.0-5787/lib/python3.9/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: 0.69 Conformation dependent library (CDL) restraints added in 256.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.85 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: 2.05 Time building geometry restraints manager: 1.01 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 I 20 " pdb=" O3' DT I 20 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" C3' DT J 41 " pdb=" C2' DT J 41 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.20e-01 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.07e-01 bond pdb=" C3' DC I -22 " pdb=" C2' DC I -22 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.00e-01 bond pdb=" C3' DG I 68 " pdb=" C2' DG I 68 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.94e-01 ... (remaining 12770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 17993 1.41 - 2.83: 482 2.83 - 4.24: 14 4.24 - 5.65: 6 5.65 - 7.06: 3 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 113.18 118.43 -5.25 2.37e+00 1.78e-01 4.91e+00 angle pdb=" CA LEU F 22 " pdb=" CB LEU F 22 " pdb=" CG LEU F 22 " ideal model delta sigma weight residual 116.30 123.36 -7.06 3.50e+00 8.16e-02 4.07e+00 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 117.81 -4.63 2.37e+00 1.78e-01 3.82e+00 angle pdb=" C3' DA I 29 " pdb=" C2' DA I 29 " pdb=" C1' DA I 29 " ideal model delta sigma weight residual 101.60 104.30 -2.70 1.50e+00 4.44e-01 3.24e+00 angle pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 122.87 -2.67 1.50e+00 4.44e-01 3.17e+00 ... (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: 1457 0.026 - 0.052: 505 0.052 - 0.078: 103 0.078 - 0.104: 24 0.104 - 0.130: 20 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: 4.070 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.610 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:6.680 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: 0.8034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12775 Z= 0.153 Angle : 0.502 7.065 18498 Z= 0.305 Chirality : 0.029 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 aren 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 covalent geometry : bond 0.00326 (12775) covalent geometry : angle 0.50160 (18498) hydrogen bonds : bond 0.23805 ( 736) hydrogen bonds : angle 8.65357 ( 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 : 0.213 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: 0.8095 (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: 0.7756 (ttpp) REVERT: E 59 GLU cc_start: 0.8053 (pm20) cc_final: 0.7844 (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: 0.6751 (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: 0.9478 time to fit residues: 162.1205 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 : 0.226 ------------------------------------------------------------------------------- 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: 4.9990 chunk 53 optimal weight: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 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 = 0.176347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134610 restraints weight = 10633.186| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 0.93 r_work: 0.3378 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12775 Z= 0.217 Angle : 0.611 7.877 18498 Z= 0.368 Chirality : 0.036 0.146 2109 Planarity : 0.005 0.041 1335 Dihedral : 30.480 179.513 4097 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.11 % Allowed : 15.98 % Favored : 79.91 % 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 aren not related in a simple way. whole: 2.51 (0.29), residues: 743 helix: 2.23 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.05 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 42 TYR 0.015 0.002 TYR B 51 PHE 0.015 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00480 (12775) covalent geometry : angle 0.61092 (18498) hydrogen bonds : bond 0.06506 ( 736) hydrogen bonds : angle 3.20933 ( 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 179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.280 Fit side-chains REVERT: A 59 GLU cc_start: 0.8589 (pm20) cc_final: 0.8356 (pm20) REVERT: A 131 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7493 (mtp180) REVERT: B 79 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8433 (mtmm) REVERT: C 36 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8255 (mmpt) REVERT: C 110 ASN cc_start: 0.8704 (t0) cc_final: 0.8346 (t0) REVERT: D 44 GLN cc_start: 0.8117 (mt0) cc_final: 0.7894 (mt0) REVERT: D 102 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: D 113 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7980 (tttm) REVERT: E 59 GLU cc_start: 0.8432 (pm20) cc_final: 0.8185 (pm20) REVERT: F 27 GLN cc_start: 0.8544 (mm110) cc_final: 0.8194 (mm110) REVERT: F 77 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8168 (mtpt) REVERT: F 93 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: G 15 LYS cc_start: 0.7577 (mtpt) cc_final: 0.6915 (tttt) REVERT: G 71 ARG cc_start: 0.7461 (ttp-110) cc_final: 0.6985 (ttm-80) REVERT: G 75 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8125 (mmtt) REVERT: G 95 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8427 (tmtm) REVERT: H 102 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: H 105 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7479 (mmtt) outliers start: 26 outliers final: 8 residues processed: 165 average time/residue: 1.0210 time to fit residues: 176.6942 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 : 0.322 ------------------------------------------------------------------------------- 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 93 GLN 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 102 GLU 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: 0.7980 chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 75 HIS C 24 GLN C 104 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 = 0.4070 r_free = 0.4070 target = 0.175241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132212 restraints weight = 10798.404| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 0.93 r_work: 0.3336 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12775 Z= 0.225 Angle : 0.611 7.922 18498 Z= 0.366 Chirality : 0.036 0.151 2109 Planarity : 0.005 0.042 1335 Dihedral : 30.776 178.001 4097 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.80 % Allowed : 15.51 % Favored : 80.70 % 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 aren not related in a simple way. whole: 2.52 (0.29), residues: 743 helix: 2.25 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.11 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 77 TYR 0.012 0.002 TYR B 51 PHE 0.014 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00503 (12775) covalent geometry : angle 0.61096 (18498) hydrogen bonds : bond 0.06434 ( 736) hydrogen bonds : angle 3.11907 ( 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 173 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.335 Fit side-chains REVERT: A 59 GLU cc_start: 0.8505 (pm20) cc_final: 0.8219 (pm20) REVERT: A 131 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7544 (mtp180) REVERT: B 79 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8403 (mtmm) REVERT: C 36 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8220 (mmpt) REVERT: C 92 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8070 (mt-10) REVERT: D 102 GLU cc_start: 0.7743 (tp30) cc_final: 0.7436 (mm-30) REVERT: D 113 LYS cc_start: 0.8582 (ttmp) cc_final: 0.8006 (tttm) REVERT: E 59 GLU cc_start: 0.8446 (pm20) cc_final: 0.8179 (pm20) REVERT: E 133 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: F 27 GLN cc_start: 0.8563 (mm110) cc_final: 0.8306 (mm110) REVERT: F 77 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8127 (mtpt) REVERT: G 15 LYS cc_start: 0.7675 (mtpt) cc_final: 0.6934 (tttt) REVERT: G 71 ARG cc_start: 0.7589 (ttp-110) cc_final: 0.7042 (ttm-80) REVERT: G 75 LYS cc_start: 0.8448 (mmtm) cc_final: 0.8226 (mmtm) REVERT: G 95 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8418 (tmtm) outliers start: 24 outliers final: 9 residues processed: 157 average time/residue: 1.0269 time to fit residues: 168.9739 Evaluate side-chains 152 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 76 GLN 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 109 SER Chi-restraints excluded: chain E residue 133 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 Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 81 ASN E 76 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133769 restraints weight = 10776.391| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 0.92 r_work: 0.3356 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12775 Z= 0.189 Angle : 0.573 7.339 18498 Z= 0.347 Chirality : 0.034 0.133 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.509 178.835 4096 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.53 % Allowed : 17.72 % Favored : 79.75 % 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 aren not related in a simple way. whole: 2.67 (0.29), residues: 743 helix: 2.37 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.11 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.012 0.002 TYR B 51 PHE 0.014 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (12775) covalent geometry : angle 0.57300 (18498) hydrogen bonds : bond 0.05530 ( 736) hydrogen bonds : angle 2.99352 ( 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 166 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.328 Fit side-chains REVERT: A 59 GLU cc_start: 0.8508 (pm20) cc_final: 0.8299 (pm20) REVERT: A 131 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7506 (mtp180) REVERT: B 52 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 79 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8420 (mtmm) REVERT: C 36 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8198 (mmpt) REVERT: D 102 GLU cc_start: 0.7676 (tp30) cc_final: 0.7422 (tp30) REVERT: D 113 LYS cc_start: 0.8592 (ttmp) cc_final: 0.8026 (tttm) REVERT: F 77 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8113 (mtpt) REVERT: F 93 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: G 15 LYS cc_start: 0.7697 (mtpt) cc_final: 0.6949 (tttt) REVERT: G 71 ARG cc_start: 0.7573 (ttp-110) cc_final: 0.7039 (ttm-80) REVERT: G 75 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8147 (mmtt) REVERT: G 95 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8370 (tmtm) REVERT: H 105 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7963 (mtmm) outliers start: 16 outliers final: 7 residues processed: 155 average time/residue: 0.9120 time to fit residues: 148.6104 Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 109 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 0.0770 chunk 31 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131918 restraints weight = 10768.551| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 0.93 r_work: 0.3329 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12775 Z= 0.233 Angle : 0.615 7.570 18498 Z= 0.367 Chirality : 0.036 0.138 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.826 176.745 4096 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.48 % Allowed : 16.93 % 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 aren not related in a simple way. whole: 2.46 (0.29), residues: 743 helix: 2.23 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.21 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 77 TYR 0.012 0.002 TYR B 51 PHE 0.014 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00524 (12775) covalent geometry : angle 0.61498 (18498) hydrogen bonds : bond 0.06332 ( 736) hydrogen bonds : angle 3.08685 ( 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 168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.387 Fit side-chains REVERT: A 59 GLU cc_start: 0.8531 (pm20) cc_final: 0.8263 (pm20) REVERT: A 131 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7518 (mtp180) REVERT: B 52 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: B 79 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8430 (mtmm) REVERT: C 36 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8234 (mmpt) REVERT: C 92 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8056 (mt-10) REVERT: D 73 GLU cc_start: 0.8636 (tp30) cc_final: 0.8321 (tp30) REVERT: D 102 GLU cc_start: 0.7735 (tp30) cc_final: 0.7488 (tp30) REVERT: E 115 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8295 (mppt) REVERT: F 27 GLN cc_start: 0.8627 (mm110) cc_final: 0.8326 (mm110) REVERT: F 77 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8146 (mtpt) REVERT: F 93 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7820 (mt0) REVERT: G 15 LYS cc_start: 0.7733 (mtpt) cc_final: 0.6954 (tttt) REVERT: G 75 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8177 (mmtt) REVERT: G 95 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8445 (tmtm) outliers start: 22 outliers final: 8 residues processed: 153 average time/residue: 0.9645 time to fit residues: 154.9580 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 : 0.221 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 115 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 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132289 restraints weight = 10591.927| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 0.96 r_work: 0.3339 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 12775 Z= 0.316 Angle : 0.693 7.845 18498 Z= 0.408 Chirality : 0.042 0.184 2109 Planarity : 0.005 0.044 1335 Dihedral : 31.390 175.452 4096 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.80 % Allowed : 16.14 % 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 aren 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 : -0.30 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 40 TYR 0.015 0.003 TYR E 54 PHE 0.016 0.002 PHE C 25 HIS 0.005 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00714 (12775) covalent geometry : angle 0.69313 (18498) hydrogen bonds : bond 0.07817 ( 736) hydrogen bonds : angle 3.22749 ( 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 165 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.344 Fit side-chains REVERT: A 131 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: B 52 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: B 79 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8428 (mtmm) REVERT: C 36 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8236 (mmpt) REVERT: C 92 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8001 (mt-10) REVERT: D 73 GLU cc_start: 0.8661 (tp30) cc_final: 0.8390 (tp30) REVERT: D 102 GLU cc_start: 0.7816 (tp30) cc_final: 0.7559 (tp30) REVERT: E 115 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8331 (mppt) REVERT: F 27 GLN cc_start: 0.8666 (mm110) cc_final: 0.8324 (mm110) REVERT: F 77 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8152 (mtpt) REVERT: F 93 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: G 15 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7066 (tttt) REVERT: G 75 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8296 (mmtt) REVERT: G 95 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8427 (tmtm) outliers start: 24 outliers final: 11 residues processed: 151 average time/residue: 1.0212 time to fit residues: 161.9152 Evaluate side-chains 155 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 30.0000 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135797 restraints weight = 10537.227| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 0.93 r_work: 0.3386 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12775 Z= 0.185 Angle : 0.597 7.759 18498 Z= 0.358 Chirality : 0.035 0.134 2109 Planarity : 0.004 0.043 1335 Dihedral : 31.138 177.310 4096 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.16 % Allowed : 16.77 % 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 aren not related in a simple way. whole: 2.53 (0.29), residues: 743 helix: 2.29 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.23 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.011 0.002 TYR B 51 PHE 0.015 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00403 (12775) covalent geometry : angle 0.59686 (18498) hydrogen bonds : bond 0.05626 ( 736) hydrogen bonds : angle 3.00374 ( 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 168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.368 Fit side-chains REVERT: A 131 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7588 (mtp180) REVERT: B 52 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: B 79 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8451 (mtmm) REVERT: C 36 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8225 (mmpt) REVERT: C 92 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7982 (mt-10) REVERT: D 82 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8321 (mtmm) REVERT: D 102 GLU cc_start: 0.7780 (tp30) cc_final: 0.7523 (tp30) REVERT: E 115 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8253 (mppt) REVERT: F 27 GLN cc_start: 0.8581 (mm110) cc_final: 0.8243 (mm110) REVERT: F 77 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8107 (mtpt) REVERT: G 15 LYS cc_start: 0.7603 (mtpt) cc_final: 0.6914 (tttt) REVERT: G 75 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8241 (mmtt) REVERT: G 95 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8355 (tmtm) outliers start: 20 outliers final: 10 residues processed: 154 average time/residue: 1.0241 time to fit residues: 165.7546 Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 115 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 109 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.174775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134049 restraints weight = 10523.616| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 0.95 r_work: 0.3362 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12775 Z= 0.233 Angle : 0.626 7.853 18498 Z= 0.374 Chirality : 0.037 0.142 2109 Planarity : 0.005 0.043 1335 Dihedral : 31.032 176.215 4096 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.01 % Allowed : 16.61 % 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 aren not related in a simple way. whole: 2.42 (0.29), residues: 743 helix: 2.20 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 20 TYR 0.012 0.002 TYR E 54 PHE 0.015 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00520 (12775) covalent geometry : angle 0.62585 (18498) hydrogen bonds : bond 0.06439 ( 736) hydrogen bonds : angle 3.07883 ( 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 164 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.330 Fit side-chains REVERT: A 131 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7562 (mtp180) REVERT: B 52 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: B 79 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8436 (mtmm) REVERT: C 36 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8219 (mmpt) REVERT: C 92 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8016 (mt-10) REVERT: D 73 GLU cc_start: 0.8633 (tp30) cc_final: 0.8353 (tp30) REVERT: E 115 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8287 (mppt) REVERT: F 27 GLN cc_start: 0.8584 (mm110) cc_final: 0.8244 (mm110) REVERT: F 77 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8170 (mtpt) REVERT: G 15 LYS cc_start: 0.7624 (mtpt) cc_final: 0.6941 (tttt) REVERT: G 75 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8181 (mmtm) REVERT: G 95 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8410 (tmtm) outliers start: 19 outliers final: 10 residues processed: 151 average time/residue: 1.0538 time to fit residues: 166.9416 Evaluate side-chains 157 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 115 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 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135691 restraints weight = 10585.771| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 0.93 r_work: 0.3383 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12775 Z= 0.170 Angle : 0.595 6.891 18498 Z= 0.359 Chirality : 0.034 0.133 2109 Planarity : 0.004 0.040 1335 Dihedral : 31.007 176.570 4096 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.69 % Allowed : 16.93 % 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 aren not related in a simple way. whole: 2.63 (0.29), residues: 743 helix: 2.36 (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 0.005 0.001 ARG C 20 TYR 0.012 0.001 TYR B 51 PHE 0.014 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00365 (12775) covalent geometry : angle 0.59529 (18498) hydrogen bonds : bond 0.05625 ( 736) hydrogen bonds : angle 3.05784 ( 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 163 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.343 Fit side-chains REVERT: A 131 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7544 (mtp180) REVERT: B 52 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: B 79 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8463 (mtmm) REVERT: C 36 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8223 (mmpt) REVERT: C 92 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7948 (mt-10) REVERT: C 110 ASN cc_start: 0.8673 (t0) cc_final: 0.8285 (t0) REVERT: D 82 LYS cc_start: 0.8635 (mmtp) cc_final: 0.8279 (mtmm) REVERT: E 115 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8257 (mppt) REVERT: F 27 GLN cc_start: 0.8570 (mm110) cc_final: 0.8230 (mm110) REVERT: F 77 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8147 (mtpt) REVERT: G 15 LYS cc_start: 0.7659 (mtpt) cc_final: 0.6926 (tttt) REVERT: G 75 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8161 (mmtm) REVERT: G 95 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8380 (tmtm) outliers start: 17 outliers final: 8 residues processed: 151 average time/residue: 1.0276 time to fit residues: 162.9700 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 : 0.353 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 115 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 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: 5.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 68 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135868 restraints weight = 10644.002| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 0.94 r_work: 0.3387 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12775 Z= 0.178 Angle : 0.591 7.510 18498 Z= 0.355 Chirality : 0.034 0.136 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.950 177.535 4096 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.04 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 aren not related in a simple way. whole: 2.69 (0.29), residues: 743 helix: 2.40 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.16 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.012 0.002 TYR B 51 PHE 0.014 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (12775) covalent geometry : angle 0.59107 (18498) hydrogen bonds : bond 0.05471 ( 736) hydrogen bonds : angle 2.99025 ( 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: 15 poor density : 145 time to evaluate : 0.295 Fit side-chains REVERT: A 131 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7530 (mtp180) REVERT: B 52 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: B 79 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8456 (mtmm) REVERT: C 36 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8222 (mmpt) REVERT: C 92 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 82 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8290 (mtmm) REVERT: E 115 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8252 (mppt) REVERT: F 27 GLN cc_start: 0.8571 (mm110) cc_final: 0.8231 (mm110) REVERT: F 77 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8133 (mtpt) REVERT: G 15 LYS cc_start: 0.7650 (mtpt) cc_final: 0.6917 (tttt) REVERT: G 75 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8171 (mmtt) REVERT: G 95 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8389 (tmtm) outliers start: 15 outliers final: 7 residues processed: 149 average time/residue: 1.0467 time to fit residues: 163.6314 Evaluate side-chains 155 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 115 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 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: 1.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 68 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.172325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.131798 restraints weight = 10523.825| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 0.97 r_work: 0.3331 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 12775 Z= 0.351 Angle : 0.728 8.092 18498 Z= 0.425 Chirality : 0.044 0.204 2109 Planarity : 0.006 0.045 1335 Dihedral : 31.424 174.693 4096 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.01 % Allowed : 17.09 % Favored : 79.91 % 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 aren not related in a simple way. whole: 2.09 (0.29), residues: 743 helix: 1.96 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.34 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 40 TYR 0.016 0.003 TYR E 54 PHE 0.017 0.003 PHE C 25 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00797 (12775) covalent geometry : angle 0.72848 (18498) hydrogen bonds : bond 0.08333 ( 736) hydrogen bonds : angle 3.27722 ( 1861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5507.43 seconds wall clock time: 94 minutes 14.23 seconds (5654.23 seconds total)