Starting phenix.real_space_refine on Fri Jul 3 04:35:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yc_75524/07_2026/10yc_75524.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yc_75524/07_2026/10yc_75524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10yc_75524/07_2026/10yc_75524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yc_75524/07_2026/10yc_75524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10yc_75524/07_2026/10yc_75524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yc_75524/07_2026/10yc_75524.map" } resolution = 2.7 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= 0.005 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 294 5.49 5 S 10 5.16 5 C 6625 2.51 5 N 2250 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11998 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "K" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2312 Classifications: {'DNA': 112} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 111} Time building chain proxies: 1.90, per 1000 atoms: 0.16 Number of scatterers: 11998 At special positions: 0 Unit cell: (74.328, 123.88, 116.708, 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 10 16.00 P 294 15.00 O 2819 8.00 N 2250 7.00 C 6625 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: 0.75 Conformation dependent library (CDL) restraints added in 268.3 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 72.5% alpha, 2.7% beta 146 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 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 removed outlier: 3.586A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) 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 37 removed outlier: 3.657A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.349A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.507A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.778A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.575A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) 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: 4.390A 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 removed outlier: 3.575A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.163A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.292A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 'E' and resid 83 through 84 removed outlier: 6.986A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.276A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 401 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2098 1.33 - 1.45: 4255 1.45 - 1.57: 5852 1.57 - 1.69: 585 1.69 - 1.80: 20 Bond restraints: 12810 Sorted by residual: bond pdb=" C3' DG K 52 " pdb=" C2' DG K 52 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C5' DA I 120 " pdb=" C4' DA I 120 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 1.01e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.83e+00 bond pdb=" C3' DG I 55 " pdb=" C2' DG I 55 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.76e+00 bond pdb=" C5' DG I 121 " pdb=" C4' DG I 121 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.61e+00 ... (remaining 12805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 16803 1.31 - 2.62: 1566 2.62 - 3.93: 169 3.93 - 5.24: 14 5.24 - 6.54: 7 Bond angle restraints: 18559 Sorted by residual: angle pdb=" N3 DT K 50 " pdb=" C4 DT K 50 " pdb=" O4 DT K 50 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 75 " pdb=" C4 DT I 75 " pdb=" O4 DT I 75 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 18554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.62: 5072 28.62 - 57.24: 1730 57.24 - 85.87: 135 85.87 - 114.49: 4 114.49 - 143.11: 3 Dihedral angle restraints: 6944 sinusoidal: 4763 harmonic: 2181 Sorted by residual: dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 76.89 143.11 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1260 0.035 - 0.071: 615 0.071 - 0.106: 177 0.106 - 0.141: 58 0.141 - 0.177: 3 Chirality restraints: 2113 Sorted by residual: chirality pdb=" C3' DC K 126 " pdb=" C4' DC K 126 " pdb=" O3' DC K 126 " pdb=" C2' DC K 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA GLN H 47 " pdb=" N GLN H 47 " pdb=" C GLN H 47 " pdb=" CB GLN H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA GLN E 68 " pdb=" N GLN E 68 " pdb=" C GLN E 68 " pdb=" CB GLN E 68 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 2110 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" CG ASP F 24 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C GLU F 63 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU F 63 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN F 64 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LYS F 59 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS F 59 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL F 60 " 0.012 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 5158 2.98 - 3.46: 11154 3.46 - 3.94: 24924 3.94 - 4.42: 27588 4.42 - 4.90: 36137 Nonbonded interactions: 104961 Sorted by model distance: nonbonded pdb=" O5' DA I 124 " pdb=" O4' DA I 124 " model vdw 2.505 2.432 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.569 3.040 nonbonded pdb=" N ILE G 79 " pdb=" O ILE G 79 " model vdw 2.576 2.496 nonbonded pdb=" N ILE C 79 " pdb=" O ILE C 79 " model vdw 2.584 2.496 nonbonded pdb=" N1 DG K 67 " pdb=" C4 DG K 67 " model vdw 2.594 2.672 ... (remaining 104956 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) 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: 5.720 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.920 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 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 0.034 12810 Z= 0.529 Angle : 0.772 6.544 18559 Z= 0.689 Chirality : 0.045 0.177 2113 Planarity : 0.005 0.043 1328 Dihedral : 28.350 143.110 5538 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.16 % Allowed : 20.48 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.30), residues: 737 helix: 1.58 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 42 TYR 0.017 0.002 TYR F 88 PHE 0.008 0.002 PHE C 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.53 (12810) covalent geometry : angle 0.77169 / 0.69 (18559) hydrogen bonds : bond 0.10899 / 6.95 ( 775) hydrogen bonds : angle 4.33173 / 3.00 ( 1939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.274 Fit side-chains REVERT: A 42 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7728 (mtp-110) REVERT: A 57 SER cc_start: 0.9056 (t) cc_final: 0.8814 (t) REVERT: A 59 GLU cc_start: 0.8084 (pt0) cc_final: 0.7828 (pm20) REVERT: C 73 ASN cc_start: 0.8694 (t0) cc_final: 0.8138 (t0) REVERT: D 108 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8734 (mtpm) REVERT: E 59 GLU cc_start: 0.8710 (pm20) cc_final: 0.8142 (pm20) REVERT: G 73 ASN cc_start: 0.8482 (t160) cc_final: 0.8107 (t160) REVERT: G 90 ASP cc_start: 0.8830 (t70) cc_final: 0.8483 (t0) REVERT: H 108 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8444 (mtpm) outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.7192 time to fit residues: 122.8256 Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.106973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.068465 restraints weight = 20084.444| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.53 r_work: 0.2763 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12810 Z= 0.171 Angle : 0.620 6.636 18559 Z= 0.378 Chirality : 0.046 0.213 2113 Planarity : 0.004 0.052 1328 Dihedral : 30.708 145.301 4051 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 18.24 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.30), residues: 737 helix: 2.17 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.65 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.019 0.001 TYR H 42 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (12810) covalent geometry : angle 0.62011 / 0.38 (18559) hydrogen bonds : bond 0.04875 / 3.32 ( 775) hydrogen bonds : angle 3.34746 / 2.29 ( 1939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.196 Fit side-chains REVERT: A 57 SER cc_start: 0.9103 (t) cc_final: 0.8786 (t) REVERT: A 59 GLU cc_start: 0.8075 (pt0) cc_final: 0.7821 (pm20) REVERT: C 73 ASN cc_start: 0.8689 (t0) cc_final: 0.8139 (t0) REVERT: D 108 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8538 (mtpm) REVERT: E 59 GLU cc_start: 0.8611 (pm20) cc_final: 0.7952 (pm20) REVERT: G 73 ASN cc_start: 0.8413 (t0) cc_final: 0.7971 (t160) REVERT: G 90 ASP cc_start: 0.8550 (t70) cc_final: 0.8206 (t0) REVERT: H 93 GLU cc_start: 0.9109 (mp0) cc_final: 0.8905 (mp0) outliers start: 10 outliers final: 7 residues processed: 160 average time/residue: 0.7643 time to fit residues: 129.1958 Evaluate side-chains 161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.066527 restraints weight = 20359.183| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.57 r_work: 0.2695 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12810 Z= 0.194 Angle : 0.613 6.620 18559 Z= 0.366 Chirality : 0.044 0.218 2113 Planarity : 0.004 0.045 1328 Dihedral : 31.062 146.001 4051 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.88 % Allowed : 17.28 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.31), residues: 737 helix: 2.37 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.58 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 86 TYR 0.019 0.002 TYR H 42 PHE 0.011 0.002 PHE C 25 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (12810) covalent geometry : angle 0.61254 / 0.37 (18559) hydrogen bonds : bond 0.04491 / 3.08 ( 775) hydrogen bonds : angle 3.04808 / 2.09 ( 1939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.293 Fit side-chains REVERT: A 57 SER cc_start: 0.9061 (t) cc_final: 0.8753 (t) REVERT: A 59 GLU cc_start: 0.8046 (pt0) cc_final: 0.7827 (pm20) REVERT: C 73 ASN cc_start: 0.8689 (t0) cc_final: 0.8139 (t0) REVERT: D 108 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8565 (mtpm) REVERT: E 59 GLU cc_start: 0.8628 (pm20) cc_final: 0.7940 (pm20) REVERT: G 73 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8012 (t160) REVERT: G 90 ASP cc_start: 0.8518 (t70) cc_final: 0.8278 (t0) outliers start: 18 outliers final: 13 residues processed: 158 average time/residue: 0.7909 time to fit residues: 131.9724 Evaluate side-chains 162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.065776 restraints weight = 20056.602| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.54 r_work: 0.2674 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12810 Z= 0.217 Angle : 0.629 7.102 18559 Z= 0.366 Chirality : 0.045 0.234 2113 Planarity : 0.004 0.047 1328 Dihedral : 31.428 147.957 4051 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.72 % Allowed : 18.08 % Favored : 79.20 % 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: 2.63 (0.31), residues: 737 helix: 2.47 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.59 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 86 TYR 0.017 0.002 TYR H 42 PHE 0.011 0.002 PHE C 25 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (12810) covalent geometry : angle 0.62908 / 0.37 (18559) hydrogen bonds : bond 0.04517 / 3.11 ( 775) hydrogen bonds : angle 2.97707 / 2.06 ( 1939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.297 Fit side-chains REVERT: C 73 ASN cc_start: 0.8704 (t0) cc_final: 0.8163 (t0) REVERT: D 108 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8571 (mtpm) REVERT: E 59 GLU cc_start: 0.8706 (pm20) cc_final: 0.8030 (pm20) REVERT: G 73 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8038 (t160) REVERT: G 90 ASP cc_start: 0.8496 (t70) cc_final: 0.8271 (t0) outliers start: 17 outliers final: 12 residues processed: 153 average time/residue: 0.8316 time to fit residues: 133.8921 Evaluate side-chains 160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.065856 restraints weight = 20171.241| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.55 r_work: 0.2678 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12810 Z= 0.174 Angle : 0.614 7.355 18559 Z= 0.361 Chirality : 0.044 0.233 2113 Planarity : 0.004 0.046 1328 Dihedral : 31.438 147.697 4049 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.04 % Allowed : 17.76 % Favored : 79.20 % 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: 2.77 (0.31), residues: 737 helix: 2.58 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.55 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 86 TYR 0.017 0.002 TYR H 42 PHE 0.010 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (12810) covalent geometry : angle 0.61427 / 0.36 (18559) hydrogen bonds : bond 0.04267 / 2.95 ( 775) hydrogen bonds : angle 2.95704 / 2.04 ( 1939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.227 Fit side-chains REVERT: B 92 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8222 (ttp80) REVERT: C 73 ASN cc_start: 0.8690 (t0) cc_final: 0.8147 (t0) REVERT: D 108 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8560 (mtpm) REVERT: E 59 GLU cc_start: 0.8671 (pm20) cc_final: 0.7997 (pm20) REVERT: G 73 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8026 (t160) REVERT: G 90 ASP cc_start: 0.8476 (t70) cc_final: 0.8244 (t0) REVERT: H 93 GLU cc_start: 0.9173 (mp0) cc_final: 0.8921 (mp0) outliers start: 19 outliers final: 15 residues processed: 155 average time/residue: 0.8046 time to fit residues: 131.5900 Evaluate side-chains 165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.066068 restraints weight = 20085.928| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.55 r_work: 0.2692 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12810 Z= 0.155 Angle : 0.606 7.218 18559 Z= 0.357 Chirality : 0.043 0.235 2113 Planarity : 0.004 0.045 1328 Dihedral : 31.427 147.368 4049 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.72 % Allowed : 18.08 % Favored : 79.20 % 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: 2.84 (0.31), residues: 737 helix: 2.64 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.016 0.001 TYR H 42 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (12810) covalent geometry : angle 0.60599 / 0.36 (18559) hydrogen bonds : bond 0.04091 / 2.82 ( 775) hydrogen bonds : angle 2.93146 / 2.02 ( 1939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.296 Fit side-chains REVERT: B 92 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8206 (ttp80) REVERT: C 73 ASN cc_start: 0.8688 (t0) cc_final: 0.8140 (t0) REVERT: D 108 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8529 (mtpm) REVERT: E 59 GLU cc_start: 0.8648 (pm20) cc_final: 0.7978 (pm20) REVERT: G 73 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8021 (t160) REVERT: G 90 ASP cc_start: 0.8464 (t70) cc_final: 0.8232 (t0) outliers start: 17 outliers final: 11 residues processed: 157 average time/residue: 0.8320 time to fit residues: 137.6861 Evaluate side-chains 159 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.066601 restraints weight = 19987.189| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.55 r_work: 0.2695 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12810 Z= 0.146 Angle : 0.600 7.251 18559 Z= 0.355 Chirality : 0.043 0.237 2113 Planarity : 0.004 0.044 1328 Dihedral : 31.408 146.856 4049 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.24 % Allowed : 18.72 % Favored : 79.04 % 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: 2.88 (0.31), residues: 737 helix: 2.66 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.49 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 79 TYR 0.018 0.001 TYR H 42 PHE 0.010 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (12810) covalent geometry : angle 0.60049 / 0.36 (18559) hydrogen bonds : bond 0.03950 / 2.73 ( 775) hydrogen bonds : angle 2.90895 / 2.00 ( 1939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.298 Fit side-chains REVERT: B 92 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8207 (ttp80) REVERT: C 73 ASN cc_start: 0.8687 (t0) cc_final: 0.8142 (t0) REVERT: D 108 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8530 (mtpm) REVERT: E 59 GLU cc_start: 0.8637 (pm20) cc_final: 0.7965 (pm20) REVERT: G 73 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8015 (t160) REVERT: G 90 ASP cc_start: 0.8439 (t70) cc_final: 0.8229 (t0) REVERT: H 93 GLU cc_start: 0.9148 (mp0) cc_final: 0.8912 (mp0) REVERT: H 99 ARG cc_start: 0.8949 (mtm110) cc_final: 0.8709 (mtp180) outliers start: 14 outliers final: 11 residues processed: 154 average time/residue: 0.7930 time to fit residues: 128.6307 Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 0.0020 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 5.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062984 restraints weight = 20029.980| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.68 r_work: 0.2611 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 12810 Z= 0.429 Angle : 0.754 8.271 18559 Z= 0.415 Chirality : 0.054 0.245 2113 Planarity : 0.006 0.049 1328 Dihedral : 31.864 152.565 4049 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.40 % Allowed : 18.08 % Favored : 79.52 % 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: 2.17 (0.30), residues: 737 helix: 2.21 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.99 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 79 TYR 0.024 0.002 TYR H 42 PHE 0.014 0.003 PHE C 25 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00949 / 0.43 (12810) covalent geometry : angle 0.75372 / 0.41 (18559) hydrogen bonds : bond 0.06503 / 4.46 ( 775) hydrogen bonds : angle 3.13326 / 2.18 ( 1939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.265 Fit side-chains REVERT: A 59 GLU cc_start: 0.8504 (pm20) cc_final: 0.7729 (pm20) REVERT: C 73 ASN cc_start: 0.8693 (t0) cc_final: 0.8168 (t0) REVERT: D 108 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8610 (mtpm) REVERT: E 59 GLU cc_start: 0.8764 (pm20) cc_final: 0.8027 (pm20) REVERT: F 91 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8757 (ttpp) REVERT: G 73 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8166 (t160) REVERT: G 90 ASP cc_start: 0.8540 (t70) cc_final: 0.8153 (t0) outliers start: 15 outliers final: 13 residues processed: 150 average time/residue: 0.8120 time to fit residues: 128.1441 Evaluate side-chains 154 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 25 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.065164 restraints weight = 19890.208| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.54 r_work: 0.2668 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12810 Z= 0.150 Angle : 0.640 7.557 18559 Z= 0.368 Chirality : 0.045 0.249 2113 Planarity : 0.004 0.049 1328 Dihedral : 31.789 149.531 4049 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.08 % Allowed : 18.72 % Favored : 79.20 % 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: 2.54 (0.31), residues: 737 helix: 2.44 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.71 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.020 0.002 TYR H 42 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (12810) covalent geometry : angle 0.63996 / 0.37 (18559) hydrogen bonds : bond 0.04165 / 2.88 ( 775) hydrogen bonds : angle 2.97192 / 2.05 ( 1939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.196 Fit side-chains REVERT: A 59 GLU cc_start: 0.8423 (pm20) cc_final: 0.7737 (pm20) REVERT: B 92 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8210 (ttp80) REVERT: C 73 ASN cc_start: 0.8679 (t0) cc_final: 0.8159 (t0) REVERT: D 108 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8561 (mtpm) REVERT: E 59 GLU cc_start: 0.8697 (pm20) cc_final: 0.8004 (pm20) REVERT: G 73 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8144 (t160) REVERT: G 90 ASP cc_start: 0.8490 (t70) cc_final: 0.8269 (t0) REVERT: H 93 GLU cc_start: 0.9204 (mp0) cc_final: 0.8966 (mp0) REVERT: H 99 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8304 (mtt-85) outliers start: 13 outliers final: 10 residues processed: 152 average time/residue: 0.8141 time to fit residues: 130.3644 Evaluate side-chains 156 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.066151 restraints weight = 20097.343| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.54 r_work: 0.2687 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12810 Z= 0.139 Angle : 0.615 7.633 18559 Z= 0.359 Chirality : 0.044 0.250 2113 Planarity : 0.004 0.051 1328 Dihedral : 31.658 147.307 4049 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.08 % Allowed : 19.04 % Favored : 78.88 % 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: 2.74 (0.31), residues: 737 helix: 2.57 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.57 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 23 TYR 0.019 0.002 TYR H 42 PHE 0.012 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (12810) covalent geometry : angle 0.61487 / 0.36 (18559) hydrogen bonds : bond 0.03822 / 2.64 ( 775) hydrogen bonds : angle 2.90926 / 2.00 ( 1939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.298 Fit side-chains REVERT: A 42 ARG cc_start: 0.8114 (mtp-110) cc_final: 0.7810 (mtp-110) REVERT: A 59 GLU cc_start: 0.8348 (pm20) cc_final: 0.7700 (pm20) REVERT: B 92 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8178 (ttp80) REVERT: C 73 ASN cc_start: 0.8674 (t0) cc_final: 0.8153 (t0) REVERT: D 108 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8504 (mtpm) REVERT: E 59 GLU cc_start: 0.8650 (pm20) cc_final: 0.8001 (pm20) REVERT: G 73 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8132 (t160) REVERT: G 90 ASP cc_start: 0.8440 (t70) cc_final: 0.8195 (t0) REVERT: H 93 GLU cc_start: 0.9206 (mp0) cc_final: 0.8974 (mp0) REVERT: H 99 ARG cc_start: 0.8953 (mtm110) cc_final: 0.8709 (mtp180) outliers start: 13 outliers final: 10 residues processed: 153 average time/residue: 0.8267 time to fit residues: 133.2517 Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.066595 restraints weight = 20186.275| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.55 r_work: 0.2708 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12810 Z= 0.153 Angle : 0.587 6.768 18559 Z= 0.349 Chirality : 0.043 0.268 2113 Planarity : 0.004 0.053 1328 Dihedral : 31.481 146.427 4049 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.08 % Allowed : 18.88 % Favored : 79.04 % 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: 2.88 (0.31), residues: 737 helix: 2.67 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.53 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.014 0.001 TYR H 42 PHE 0.011 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (12810) covalent geometry : angle 0.58749 / 0.35 (18559) hydrogen bonds : bond 0.03851 / 2.66 ( 775) hydrogen bonds : angle 2.82116 / 1.93 ( 1939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4289.64 seconds wall clock time: 73 minutes 32.58 seconds (4412.58 seconds total)