Starting phenix.real_space_refine on Sun Apr 5 17:14:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yc_75524/04_2026/10yc_75524.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yc_75524/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/10yc_75524/04_2026/10yc_75524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yc_75524/04_2026/10yc_75524.map" model { file = "/net/cci-nas-00/data/ceres_data/10yc_75524/04_2026/10yc_75524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yc_75524/04_2026/10yc_75524.cif" } 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-2.1rc1-6017/lib/python3.9/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: 2.63, per 1000 atoms: 0.22 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: 0.97 Conformation dependent library (CDL) restraints added in 399.3 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: 2.09 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: 2.37 Time building geometry restraints manager: 1.35 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=" N LEU H 101 " pdb=" CA LEU H 101 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.24e-02 6.50e+03 6.15e+00 bond pdb=" N GLN E 68 " pdb=" CA GLN E 68 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.49e+00 bond pdb=" N GLN H 47 " pdb=" CA GLN H 47 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.23e-02 6.61e+03 3.28e+00 bond pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.32e-02 5.74e+03 2.86e+00 bond pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 1.531 1.555 -0.024 1.51e-02 4.39e+03 2.62e+00 ... (remaining 12805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 17658 1.31 - 2.62: 818 2.62 - 3.93: 65 3.93 - 5.24: 11 5.24 - 6.54: 7 Bond angle restraints: 18559 Sorted by residual: angle pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " pdb=" CG ASP F 24 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C ASP F 24 " pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 111.51 116.82 -5.31 1.58e+00 4.01e-01 1.13e+01 angle pdb=" CA LEU H 101 " pdb=" C LEU H 101 " pdb=" O LEU H 101 " ideal model delta sigma weight residual 120.55 117.45 3.10 1.07e+00 8.73e-01 8.40e+00 angle pdb=" N ASP F 24 " pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 112.30 108.04 4.26 1.52e+00 4.33e-01 7.87e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.72 -6.54 2.37e+00 1.78e-01 7.62e+00 ... (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 - 0.034: 1478 0.034 - 0.068: 505 0.068 - 0.102: 83 0.102 - 0.136: 44 0.136 - 0.170: 3 Chirality restraints: 2113 Sorted by residual: 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 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.820 Find NCS groups from input model: 0.110 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:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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 : 0.004 0.038 12810 Z= 0.183 Angle : 0.607 6.544 18559 Z= 0.370 Chirality : 0.037 0.170 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 covalent geometry : bond 0.00391 (12810) covalent geometry : angle 0.60673 (18559) hydrogen bonds : bond 0.10899 ( 775) hydrogen bonds : angle 4.33173 ( 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 : 0.393 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: 0.9257 time to fit residues: 157.6808 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 : 0.369 ------------------------------------------------------------------------------- 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: 4.9990 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: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3606 r_free = 0.3606 target = 0.106657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.067932 restraints weight = 20106.407| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.55 r_work: 0.2758 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12810 Z= 0.196 Angle : 0.565 6.794 18559 Z= 0.343 Chirality : 0.034 0.145 2113 Planarity : 0.004 0.054 1328 Dihedral : 30.607 143.567 4051 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.60 % Allowed : 18.40 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.30), residues: 737 helix: 2.16 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.018 0.001 TYR H 42 PHE 0.016 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00436 (12810) covalent geometry : angle 0.56543 (18559) hydrogen bonds : bond 0.04381 ( 775) hydrogen bonds : angle 3.31811 ( 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 166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.312 Fit side-chains REVERT: A 56 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8688 (ttpp) REVERT: A 57 SER cc_start: 0.9118 (t) cc_final: 0.8803 (t) REVERT: A 59 GLU cc_start: 0.8095 (pt0) cc_final: 0.7840 (pm20) REVERT: C 73 ASN cc_start: 0.8689 (t0) cc_final: 0.8142 (t0) REVERT: D 108 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8534 (mtpm) REVERT: E 59 GLU cc_start: 0.8626 (pm20) cc_final: 0.7974 (pm20) REVERT: G 73 ASN cc_start: 0.8410 (t160) cc_final: 0.7970 (t160) REVERT: G 90 ASP cc_start: 0.8586 (t70) cc_final: 0.8211 (t0) REVERT: H 99 ARG cc_start: 0.8876 (mtm110) cc_final: 0.8297 (mtt-85) outliers start: 10 outliers final: 6 residues processed: 158 average time/residue: 0.9180 time to fit residues: 152.7312 Evaluate side-chains 162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 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: 0.8980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 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 = 0.3606 r_free = 0.3606 target = 0.106601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068057 restraints weight = 20405.181| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.55 r_work: 0.2759 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12810 Z= 0.190 Angle : 0.552 6.733 18559 Z= 0.337 Chirality : 0.033 0.131 2113 Planarity : 0.004 0.047 1328 Dihedral : 30.600 144.069 4051 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.40 % Allowed : 17.76 % 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: 2.31 (0.30), residues: 737 helix: 2.25 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.015 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 covalent geometry : bond 0.00420 (12810) covalent geometry : angle 0.55205 (18559) hydrogen bonds : bond 0.04139 ( 775) hydrogen bonds : angle 3.15121 ( 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 171 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.324 Fit side-chains REVERT: A 57 SER cc_start: 0.9103 (t) cc_final: 0.8795 (t) REVERT: A 59 GLU cc_start: 0.8016 (pt0) cc_final: 0.7807 (pm20) REVERT: C 73 ASN cc_start: 0.8678 (t0) cc_final: 0.8120 (t0) REVERT: D 108 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8555 (mtpm) REVERT: E 59 GLU cc_start: 0.8612 (pm20) cc_final: 0.7949 (pm20) REVERT: G 73 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7972 (t160) REVERT: G 90 ASP cc_start: 0.8577 (t70) cc_final: 0.8213 (t0) outliers start: 15 outliers final: 10 residues processed: 162 average time/residue: 0.8932 time to fit residues: 152.3927 Evaluate side-chains 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 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 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: 0.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3612 r_free = 0.3612 target = 0.107024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.068175 restraints weight = 20126.474| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.55 r_work: 0.2730 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0562 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= 0.162 Angle : 0.539 6.781 18559 Z= 0.330 Chirality : 0.033 0.129 2113 Planarity : 0.004 0.046 1328 Dihedral : 30.605 144.209 4051 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.08 % Allowed : 18.40 % 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: 2.50 (0.31), residues: 737 helix: 2.38 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.017 0.001 TYR H 42 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00345 (12810) covalent geometry : angle 0.53866 (18559) hydrogen bonds : bond 0.03915 ( 775) hydrogen bonds : angle 3.11537 ( 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 166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.202 Fit side-chains REVERT: A 56 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8785 (ttpp) REVERT: A 57 SER cc_start: 0.9107 (t) cc_final: 0.8830 (t) REVERT: A 59 GLU cc_start: 0.8022 (pt0) cc_final: 0.7821 (pm20) REVERT: C 73 ASN cc_start: 0.8688 (t0) cc_final: 0.8131 (t0) REVERT: D 108 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8543 (mtpm) REVERT: E 59 GLU cc_start: 0.8613 (pm20) cc_final: 0.7939 (pm20) REVERT: G 73 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7980 (t160) REVERT: G 90 ASP cc_start: 0.8539 (t70) cc_final: 0.8169 (t0) REVERT: H 93 GLU cc_start: 0.9141 (mp0) cc_final: 0.8930 (mp0) outliers start: 13 outliers final: 10 residues processed: 158 average time/residue: 0.9163 time to fit residues: 152.3872 Evaluate side-chains 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3600 r_free = 0.3600 target = 0.106158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.067169 restraints weight = 20210.354| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.56 r_work: 0.2711 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12810 Z= 0.216 Angle : 0.554 6.368 18559 Z= 0.336 Chirality : 0.034 0.129 2113 Planarity : 0.004 0.045 1328 Dihedral : 30.595 144.880 4051 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.88 % Allowed : 17.76 % 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: 2.59 (0.31), residues: 737 helix: 2.46 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.61 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.017 0.001 TYR H 42 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00487 (12810) covalent geometry : angle 0.55381 (18559) hydrogen bonds : bond 0.03840 ( 775) hydrogen bonds : angle 3.00710 ( 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 170 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.312 Fit side-chains REVERT: A 56 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8800 (ttpp) REVERT: A 57 SER cc_start: 0.9095 (t) cc_final: 0.8794 (t) REVERT: A 120 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7850 (mtt) REVERT: C 73 ASN cc_start: 0.8702 (t0) cc_final: 0.8154 (t0) REVERT: D 108 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8579 (mtpm) REVERT: E 59 GLU cc_start: 0.8622 (pm20) cc_final: 0.7956 (pm20) REVERT: G 73 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7997 (t160) REVERT: G 90 ASP cc_start: 0.8508 (t70) cc_final: 0.8267 (t0) outliers start: 18 outliers final: 12 residues processed: 159 average time/residue: 0.9023 time to fit residues: 151.1012 Evaluate side-chains 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 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 = 0.3611 r_free = 0.3611 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.068252 restraints weight = 20096.027| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.54 r_work: 0.2734 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12810 Z= 0.158 Angle : 0.534 6.793 18559 Z= 0.328 Chirality : 0.032 0.132 2113 Planarity : 0.004 0.043 1328 Dihedral : 30.634 144.931 4051 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.40 % Allowed : 18.40 % 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: 2.85 (0.31), residues: 737 helix: 2.71 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.51 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 86 TYR 0.016 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 covalent geometry : bond 0.00339 (12810) covalent geometry : angle 0.53416 (18559) hydrogen bonds : bond 0.03672 ( 775) hydrogen bonds : angle 2.96803 ( 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 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.367 Fit side-chains REVERT: A 57 SER cc_start: 0.8947 (t) cc_final: 0.8668 (t) REVERT: A 59 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: A 120 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7785 (mtt) REVERT: C 73 ASN cc_start: 0.8690 (t0) cc_final: 0.8138 (t0) REVERT: D 108 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8547 (mtpm) REVERT: E 59 GLU cc_start: 0.8605 (pm20) cc_final: 0.7947 (pm20) REVERT: G 73 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7986 (t160) REVERT: G 90 ASP cc_start: 0.8484 (t70) cc_final: 0.8253 (t0) REVERT: H 93 GLU cc_start: 0.9114 (mp0) cc_final: 0.8888 (mp0) outliers start: 15 outliers final: 10 residues processed: 152 average time/residue: 0.9550 time to fit residues: 152.5732 Evaluate side-chains 161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET 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 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 0.0570 chunk 58 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3613 r_free = 0.3613 target = 0.106964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.068126 restraints weight = 20021.955| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.54 r_work: 0.2733 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12810 Z= 0.156 Angle : 0.531 6.928 18559 Z= 0.326 Chirality : 0.032 0.127 2113 Planarity : 0.004 0.055 1328 Dihedral : 30.623 144.973 4051 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.24 % Allowed : 18.40 % 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: 2.90 (0.31), residues: 737 helix: 2.74 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.48 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 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 covalent geometry : bond 0.00336 (12810) covalent geometry : angle 0.53141 (18559) hydrogen bonds : bond 0.03538 ( 775) hydrogen bonds : angle 2.92619 ( 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 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.296 Fit side-chains REVERT: A 56 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8709 (ttpp) REVERT: A 57 SER cc_start: 0.8953 (t) cc_final: 0.8696 (t) REVERT: A 59 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: C 73 ASN cc_start: 0.8687 (t0) cc_final: 0.8131 (t0) REVERT: D 108 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8539 (mtpm) REVERT: E 59 GLU cc_start: 0.8579 (pm20) cc_final: 0.7916 (pm20) REVERT: G 73 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7987 (t160) REVERT: G 90 ASP cc_start: 0.8451 (t70) cc_final: 0.8239 (t0) outliers start: 14 outliers final: 8 residues processed: 155 average time/residue: 0.9412 time to fit residues: 153.3126 Evaluate side-chains 159 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 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 = 0.3549 r_free = 0.3549 target = 0.102938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.063802 restraints weight = 20076.187| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.60 r_work: 0.2634 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.051 12810 Z= 0.380 Angle : 0.636 7.380 18559 Z= 0.377 Chirality : 0.042 0.161 2113 Planarity : 0.005 0.048 1328 Dihedral : 31.206 150.267 4051 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.88 % Allowed : 18.24 % 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: 2.50 (0.30), residues: 737 helix: 2.51 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 86 TYR 0.019 0.002 TYR H 42 PHE 0.016 0.003 PHE C 25 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00877 (12810) covalent geometry : angle 0.63584 (18559) hydrogen bonds : bond 0.05415 ( 775) hydrogen bonds : angle 3.06579 ( 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 161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.305 Fit side-chains REVERT: C 73 ASN cc_start: 0.8698 (t0) cc_final: 0.8171 (t0) REVERT: D 108 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8598 (mtpm) REVERT: E 59 GLU cc_start: 0.8776 (pm20) cc_final: 0.8071 (pm20) REVERT: G 73 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8082 (t160) REVERT: G 90 ASP cc_start: 0.8546 (t70) cc_final: 0.8148 (t0) outliers start: 18 outliers final: 12 residues processed: 150 average time/residue: 0.9807 time to fit residues: 154.3169 Evaluate side-chains 155 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL 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: 0.7980 chunk 83 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3610 r_free = 0.3610 target = 0.106736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.068243 restraints weight = 20017.335| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.53 r_work: 0.2735 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12810 Z= 0.163 Angle : 0.531 6.588 18559 Z= 0.326 Chirality : 0.033 0.130 2113 Planarity : 0.004 0.047 1328 Dihedral : 30.811 145.603 4051 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.92 % Allowed : 19.52 % Favored : 78.56 % 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: 2.92 (0.31), residues: 737 helix: 2.79 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.58 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.015 0.001 TYR F 88 PHE 0.010 0.001 PHE A 67 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00359 (12810) covalent geometry : angle 0.53135 (18559) hydrogen bonds : bond 0.03303 ( 775) hydrogen bonds : angle 2.77931 ( 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 166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.323 Fit side-chains REVERT: A 56 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8641 (ttpp) REVERT: A 59 GLU cc_start: 0.8298 (pm20) cc_final: 0.7723 (pm20) REVERT: C 73 ASN cc_start: 0.8668 (t0) cc_final: 0.8139 (t0) REVERT: D 108 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8473 (mtpm) REVERT: E 59 GLU cc_start: 0.8553 (pm20) cc_final: 0.7861 (pm20) REVERT: G 73 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8022 (t160) REVERT: H 93 GLU cc_start: 0.9202 (mp0) cc_final: 0.8997 (mp0) outliers start: 12 outliers final: 7 residues processed: 160 average time/residue: 0.9607 time to fit residues: 161.5304 Evaluate side-chains 157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 93 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.106989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.068107 restraints weight = 20211.689| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.56 r_work: 0.2735 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12810 Z= 0.156 Angle : 0.537 6.785 18559 Z= 0.330 Chirality : 0.033 0.127 2113 Planarity : 0.004 0.046 1328 Dihedral : 30.825 145.549 4049 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.60 % Allowed : 20.00 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.31), residues: 737 helix: 2.85 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.018 0.001 TYR H 42 PHE 0.011 0.001 PHE A 67 HIS 0.002 0.000 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00337 (12810) covalent geometry : angle 0.53668 (18559) hydrogen bonds : bond 0.03187 ( 775) hydrogen bonds : angle 2.77336 ( 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 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.368 Fit side-chains REVERT: A 42 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7715 (mtp85) REVERT: A 56 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8590 (ttpp) REVERT: A 59 GLU cc_start: 0.8351 (pm20) cc_final: 0.7765 (pm20) REVERT: B 92 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8208 (ttp80) REVERT: C 73 ASN cc_start: 0.8670 (t0) cc_final: 0.8138 (t0) REVERT: D 108 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8458 (mtpm) REVERT: E 59 GLU cc_start: 0.8541 (pm20) cc_final: 0.8248 (pm20) REVERT: G 73 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8020 (t160) REVERT: G 90 ASP cc_start: 0.8572 (t0) cc_final: 0.8296 (t0) REVERT: H 93 GLU cc_start: 0.9207 (mp0) cc_final: 0.8961 (mp0) outliers start: 10 outliers final: 6 residues processed: 153 average time/residue: 0.9384 time to fit residues: 151.1201 Evaluate side-chains 154 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3614 r_free = 0.3614 target = 0.106956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.068394 restraints weight = 20201.667| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.54 r_work: 0.2738 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12810 Z= 0.163 Angle : 0.536 6.799 18559 Z= 0.328 Chirality : 0.033 0.127 2113 Planarity : 0.004 0.047 1328 Dihedral : 30.834 145.346 4049 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.92 % Allowed : 20.64 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.31), residues: 737 helix: 2.86 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.45 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.015 0.001 TYR H 42 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00357 (12810) covalent geometry : angle 0.53567 (18559) hydrogen bonds : bond 0.03273 ( 775) hydrogen bonds : angle 2.76058 ( 1939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5208.04 seconds wall clock time: 88 minutes 55.80 seconds (5335.80 seconds total)