Starting phenix.real_space_refine on Wed Aug 5 03:58:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu2_28602/08_2026/8eu2_28602_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu2_28602/08_2026/8eu2_28602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eu2_28602/08_2026/8eu2_28602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu2_28602/08_2026/8eu2_28602.map" model { file = "/net/cci-nas-00/data/ceres_data/8eu2_28602/08_2026/8eu2_28602_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu2_28602/08_2026/8eu2_28602_neut.cif" } resolution = 2.93 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= 0.014 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 218 5.49 5 S 8 5.16 5 C 4769 2.51 5 N 1634 2.21 5 O 2053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8682 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2240 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2264 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "K" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "N" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "P" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Time building chain proxies: 1.78, per 1000 atoms: 0.21 Number of scatterers: 8682 At special positions: 0 Unit cell: (121.91, 102.705, 106.045, 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 8 16.00 P 218 15.00 O 2053 8.00 N 1634 7.00 C 4769 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: 0.74 Conformation dependent library (CDL) restraints added in 335.0 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 75.4% alpha, 2.7% beta 109 base pairs and 193 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'K' and resid 63 through 76 removed outlier: 3.527A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.579A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 3.825A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 removed outlier: 3.586A pdb=" N GLY L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.888A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY L 56 " --> pdb=" O GLU L 52 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA L 76 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 46 through 73 Processing helix chain 'M' and resid 79 through 90 removed outlier: 3.586A pdb=" N ASN M 89 " --> pdb=" O LEU M 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP M 90 " --> pdb=" O ALA M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 removed outlier: 3.577A pdb=" N ASN N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 121 removed outlier: 3.656A pdb=" N ALA N 104 " --> pdb=" O PRO N 100 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 79 removed outlier: 3.688A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 removed outlier: 3.506A pdb=" N VAL O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.571A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.166A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.552A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.486A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.328A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.727A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.577A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 118 through 119 278 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 283 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 193 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 0.95 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: 1562 1.33 - 1.45: 3155 1.45 - 1.57: 4112 1.57 - 1.69: 437 1.69 - 1.81: 16 Bond restraints: 9282 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DC J -25 " pdb=" C2' DC J -25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 12466 1.83 - 3.67: 931 3.67 - 5.50: 58 5.50 - 7.33: 13 7.33 - 9.17: 9 Bond angle restraints: 13477 Sorted by residual: angle pdb=" CA PRO O 43 " pdb=" N PRO O 43 " pdb=" CD PRO O 43 " ideal model delta sigma weight residual 112.00 103.66 8.34 1.40e+00 5.10e-01 3.55e+01 angle pdb=" N GLU M 61 " pdb=" CA GLU M 61 " pdb=" CB GLU M 61 " ideal model delta sigma weight residual 110.16 117.49 -7.33 1.48e+00 4.57e-01 2.45e+01 angle pdb=" O5' DA I -54 " pdb=" C5' DA I -54 " pdb=" C4' DA I -54 " ideal model delta sigma weight residual 109.40 113.21 -3.81 8.00e-01 1.56e+00 2.27e+01 angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+01 ... (remaining 13472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 3934 34.93 - 69.86: 1057 69.86 - 104.79: 10 104.79 - 139.72: 0 139.72 - 174.65: 2 Dihedral angle restraints: 5003 sinusoidal: 3480 harmonic: 1523 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 34.65 -174.65 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 69.06 150.94 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA ILE P 29 " pdb=" C ILE P 29 " pdb=" N THR P 30 " pdb=" CA THR P 30 " ideal model delta harmonic sigma weight residual -180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1091 0.053 - 0.105: 369 0.105 - 0.158: 63 0.158 - 0.211: 9 0.211 - 0.263: 4 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA GLU M 61 " pdb=" N GLU M 61 " pdb=" C GLU M 61 " pdb=" CB GLU M 61 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU M 115 " pdb=" CB LEU M 115 " pdb=" CD1 LEU M 115 " pdb=" CD2 LEU M 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE M 79 " pdb=" N ILE M 79 " pdb=" C ILE M 79 " pdb=" CB ILE M 79 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1533 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG O 42 " 0.073 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO O 43 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO O 43 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 43 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 79 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO M 80 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 62 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ILE M 62 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE M 62 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU M 63 " 0.013 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2644 2.88 - 3.39: 7338 3.39 - 3.89: 17030 3.89 - 4.40: 18879 4.40 - 4.90: 26074 Nonbonded interactions: 71965 Sorted by model distance: nonbonded pdb=" ND2 ASN O 108 " pdb=" O GLY P 42 " model vdw 2.381 3.120 nonbonded pdb=" OE1 GLU O 50 " pdb=" NH1 ARG P 39 " model vdw 2.413 3.120 nonbonded pdb=" OE1 GLU O 73 " pdb=" ND2 ASN P 25 " model vdw 2.415 3.120 nonbonded pdb=" OP1 DC I -23 " pdb=" NH1 ARG K 72 " model vdw 2.417 3.120 nonbonded pdb=" OP1 DG J 48 " pdb=" OH TYR N 37 " model vdw 2.428 3.040 ... (remaining 71960 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 'L' and resid 24 through 94) selection = (chain 'P' and resid 24 through 94) } 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: 10.130 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.970 Find NCS groups from input model: 0.080 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.007 0.100 9282 Z= 0.599 Angle : 0.965 9.165 13477 Z= 0.781 Chirality : 0.053 0.263 1536 Planarity : 0.009 0.105 944 Dihedral : 28.134 174.646 4017 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.33), residues: 512 helix: -0.24 (0.24), residues: 379 sheet: None (None), residues: 0 loop : -1.01 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 128 TYR 0.014 0.002 TYR P 72 PHE 0.027 0.003 PHE K 78 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.60 ( 9282) covalent geometry : angle 0.96477 / 0.78 (13477) hydrogen bonds : bond 0.11358 / 12.64 ( 561) hydrogen bonds : angle 3.72919 / 4.81 ( 1382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7316 (ttp-170) REVERT: N 64 ASN cc_start: 0.8346 (m-40) cc_final: 0.8028 (m-40) REVERT: N 73 GLU cc_start: 0.7707 (tp30) cc_final: 0.7333 (tp30) REVERT: N 112 THR cc_start: 0.8772 (p) cc_final: 0.8506 (t) REVERT: O 70 LEU cc_start: 0.8505 (tp) cc_final: 0.8189 (tm) REVERT: O 116 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7860 (ttp80) REVERT: O 120 MET cc_start: 0.6907 (mtt) cc_final: 0.6515 (mtt) REVERT: O 128 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8293 (mtp180) REVERT: O 130 ILE cc_start: 0.8824 (mm) cc_final: 0.8553 (mt) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 0.6362 time to fit residues: 129.4536 Evaluate side-chains 191 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 56 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN M 68 ASN M 84 GLN M 94 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.131809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105640 restraints weight = 15837.660| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.55 r_work: 0.3419 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9282 Z= 0.179 Angle : 0.697 8.255 13477 Z= 0.415 Chirality : 0.047 0.197 1536 Planarity : 0.005 0.070 944 Dihedral : 31.071 171.993 2971 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.52 % Allowed : 18.31 % Favored : 79.18 % 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: 1.29 (0.37), residues: 512 helix: 1.35 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.53 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 63 TYR 0.016 0.001 TYR M 57 PHE 0.006 0.001 PHE K 104 HIS 0.002 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 ( 9282) covalent geometry : angle 0.69661 / 0.41 (13477) hydrogen bonds : bond 0.05865 / 6.49 ( 561) hydrogen bonds : angle 2.96048 / 3.87 ( 1382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 131 ARG cc_start: 0.8731 (ttt180) cc_final: 0.8439 (mtt-85) REVERT: M 61 GLU cc_start: 0.8017 (mp0) cc_final: 0.7694 (mp0) REVERT: M 64 GLU cc_start: 0.8234 (tp30) cc_final: 0.7844 (tp30) REVERT: M 68 ASN cc_start: 0.8471 (m-40) cc_final: 0.7187 (m110) REVERT: N 64 ASN cc_start: 0.8793 (m-40) cc_final: 0.8532 (m-40) REVERT: N 73 GLU cc_start: 0.8445 (tp30) cc_final: 0.8097 (tp30) REVERT: O 120 MET cc_start: 0.7900 (mtt) cc_final: 0.7565 (mtm) REVERT: O 129 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8250 (tmm-80) REVERT: O 130 ILE cc_start: 0.9007 (mm) cc_final: 0.8792 (mt) outliers start: 11 outliers final: 9 residues processed: 199 average time/residue: 0.5813 time to fit residues: 121.8598 Evaluate side-chains 204 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN M 94 ASN M 112 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103842 restraints weight = 15709.840| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.54 r_work: 0.3386 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9282 Z= 0.212 Angle : 0.690 7.143 13477 Z= 0.406 Chirality : 0.048 0.232 1536 Planarity : 0.005 0.062 944 Dihedral : 31.035 170.928 2968 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.12 % Allowed : 21.74 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.38), residues: 512 helix: 1.87 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 63 TYR 0.019 0.002 TYR P 88 PHE 0.011 0.001 PHE K 104 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.21 ( 9282) covalent geometry : angle 0.69027 / 0.41 (13477) hydrogen bonds : bond 0.05888 / 6.51 ( 561) hydrogen bonds : angle 2.87791 / 3.83 ( 1382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: K 131 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8440 (mtt-85) REVERT: L 88 TYR cc_start: 0.8837 (m-10) cc_final: 0.8627 (m-10) REVERT: M 61 GLU cc_start: 0.8042 (mp0) cc_final: 0.7549 (mp0) REVERT: M 64 GLU cc_start: 0.8234 (tp30) cc_final: 0.7654 (tp30) REVERT: M 68 ASN cc_start: 0.8518 (m-40) cc_final: 0.7036 (m-40) REVERT: N 39 TYR cc_start: 0.8689 (t80) cc_final: 0.8424 (t80) REVERT: N 64 ASN cc_start: 0.8813 (m-40) cc_final: 0.8545 (m-40) REVERT: O 70 LEU cc_start: 0.8873 (tp) cc_final: 0.8595 (tm) REVERT: O 116 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8451 (ttp80) REVERT: O 120 MET cc_start: 0.7941 (mtt) cc_final: 0.7583 (mtm) outliers start: 18 outliers final: 11 residues processed: 205 average time/residue: 0.5903 time to fit residues: 127.2773 Evaluate side-chains 214 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 90 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 85 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN ** O 93 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.129013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102619 restraints weight = 15923.540| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.55 r_work: 0.3374 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9282 Z= 0.210 Angle : 0.687 8.020 13477 Z= 0.402 Chirality : 0.047 0.210 1536 Planarity : 0.006 0.060 944 Dihedral : 31.020 168.763 2968 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.18 % Allowed : 23.80 % Favored : 70.02 % 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 (0.37), residues: 512 helix: 2.10 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.69 (0.51), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 71 TYR 0.024 0.002 TYR P 88 PHE 0.010 0.001 PHE K 104 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.21 ( 9282) covalent geometry : angle 0.68733 / 0.40 (13477) hydrogen bonds : bond 0.05763 / 6.37 ( 561) hydrogen bonds : angle 2.83835 / 3.82 ( 1382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: K 131 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8429 (mtt-85) REVERT: M 61 GLU cc_start: 0.8074 (mp0) cc_final: 0.7766 (mp0) REVERT: M 64 GLU cc_start: 0.8245 (tp30) cc_final: 0.7683 (tp30) REVERT: M 68 ASN cc_start: 0.8473 (m-40) cc_final: 0.7145 (m-40) REVERT: N 39 TYR cc_start: 0.8709 (t80) cc_final: 0.8454 (t80) REVERT: N 64 ASN cc_start: 0.8833 (m-40) cc_final: 0.8547 (m-40) REVERT: N 73 GLU cc_start: 0.8497 (tp30) cc_final: 0.8216 (tp30) REVERT: O 70 LEU cc_start: 0.8873 (tp) cc_final: 0.8589 (tm) REVERT: O 116 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8480 (ttp80) REVERT: O 120 MET cc_start: 0.7943 (mtt) cc_final: 0.7572 (mtm) REVERT: P 84 MET cc_start: 0.8245 (tpt) cc_final: 0.7172 (tpt) outliers start: 27 outliers final: 17 residues processed: 204 average time/residue: 0.5567 time to fit residues: 119.7220 Evaluate side-chains 219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 85 GLN K 108 ASN L 93 GLN ** O 93 GLN ** 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 = 0.3916 r_free = 0.3916 target = 0.128707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102330 restraints weight = 15787.076| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.54 r_work: 0.3372 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9282 Z= 0.202 Angle : 0.678 7.254 13477 Z= 0.397 Chirality : 0.047 0.213 1536 Planarity : 0.006 0.062 944 Dihedral : 31.013 167.431 2968 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.49 % Allowed : 25.17 % Favored : 69.34 % 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: 2.30 (0.37), residues: 512 helix: 2.21 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.67 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 20 TYR 0.013 0.002 TYR P 88 PHE 0.014 0.001 PHE K 78 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.20 ( 9282) covalent geometry : angle 0.67772 / 0.40 (13477) hydrogen bonds : bond 0.05679 / 6.28 ( 561) hydrogen bonds : angle 2.79738 / 3.77 ( 1382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: K 131 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8413 (mtt-85) REVERT: M 61 GLU cc_start: 0.8102 (mp0) cc_final: 0.7801 (mp0) REVERT: M 64 GLU cc_start: 0.8223 (tp30) cc_final: 0.7778 (tp30) REVERT: M 68 ASN cc_start: 0.8466 (m-40) cc_final: 0.7484 (m-40) REVERT: N 39 TYR cc_start: 0.8627 (t80) cc_final: 0.8411 (t80) REVERT: N 64 ASN cc_start: 0.8845 (m-40) cc_final: 0.8566 (m-40) REVERT: N 73 GLU cc_start: 0.8505 (tp30) cc_final: 0.8243 (tp30) REVERT: O 70 LEU cc_start: 0.8891 (tp) cc_final: 0.8540 (tm) REVERT: O 116 ARG cc_start: 0.8700 (ttp80) cc_final: 0.8480 (ttp80) REVERT: O 120 MET cc_start: 0.7955 (mtt) cc_final: 0.7601 (mtm) REVERT: P 91 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8569 (ttmt) outliers start: 24 outliers final: 17 residues processed: 204 average time/residue: 0.5540 time to fit residues: 119.2071 Evaluate side-chains 219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 85 GLN K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN P 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.124241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.097403 restraints weight = 15834.797| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.57 r_work: 0.3279 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 9282 Z= 0.413 Angle : 0.856 11.946 13477 Z= 0.475 Chirality : 0.058 0.226 1536 Planarity : 0.007 0.057 944 Dihedral : 31.175 157.806 2968 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.72 % Allowed : 25.63 % Favored : 68.65 % 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: 1.57 (0.36), residues: 512 helix: 1.70 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.88 (0.49), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 72 TYR 0.026 0.003 TYR P 88 PHE 0.023 0.003 PHE K 78 HIS 0.008 0.001 HIS K 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.41 ( 9282) covalent geometry : angle 0.85582 / 0.47 (13477) hydrogen bonds : bond 0.08044 / 8.79 ( 561) hydrogen bonds : angle 3.28252 / 4.44 ( 1382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: K 131 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8482 (mtt-85) REVERT: M 61 GLU cc_start: 0.8130 (mp0) cc_final: 0.7806 (mp0) REVERT: M 64 GLU cc_start: 0.8229 (tp30) cc_final: 0.7712 (tp30) REVERT: M 68 ASN cc_start: 0.8478 (m-40) cc_final: 0.7565 (m-40) REVERT: M 79 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8355 (tp) REVERT: N 64 ASN cc_start: 0.8844 (m-40) cc_final: 0.8584 (m-40) REVERT: N 76 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7932 (mtp180) REVERT: O 70 LEU cc_start: 0.8991 (tp) cc_final: 0.8662 (tm) REVERT: O 97 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8158 (mm-30) REVERT: O 120 MET cc_start: 0.8077 (mtt) cc_final: 0.7557 (mtp) outliers start: 25 outliers final: 17 residues processed: 217 average time/residue: 0.6213 time to fit residues: 142.0725 Evaluate side-chains 230 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 MET Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 85 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101689 restraints weight = 15967.461| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.53 r_work: 0.3359 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9282 Z= 0.189 Angle : 0.718 8.424 13477 Z= 0.411 Chirality : 0.049 0.220 1536 Planarity : 0.006 0.062 944 Dihedral : 31.072 161.133 2968 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.35 % Allowed : 29.29 % Favored : 66.36 % 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: 2.30 (0.37), residues: 512 helix: 2.21 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.64 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 20 TYR 0.025 0.002 TYR P 88 PHE 0.017 0.002 PHE K 78 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.19 ( 9282) covalent geometry : angle 0.71776 / 0.41 (13477) hydrogen bonds : bond 0.05923 / 6.60 ( 561) hydrogen bonds : angle 2.92715 / 3.98 ( 1382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: K 131 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8416 (mtt-85) REVERT: M 61 GLU cc_start: 0.8081 (mp0) cc_final: 0.7793 (mp0) REVERT: M 64 GLU cc_start: 0.8156 (tp30) cc_final: 0.7705 (tp30) REVERT: M 68 ASN cc_start: 0.8456 (m-40) cc_final: 0.7491 (m-40) REVERT: N 39 TYR cc_start: 0.8590 (t80) cc_final: 0.8285 (t80) REVERT: N 64 ASN cc_start: 0.8828 (m-40) cc_final: 0.8566 (m-40) REVERT: N 73 GLU cc_start: 0.8516 (tp30) cc_final: 0.8209 (tp30) REVERT: O 90 MET cc_start: 0.8579 (mpp) cc_final: 0.8377 (mmt) REVERT: O 97 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8099 (mm-30) REVERT: O 120 MET cc_start: 0.7940 (mtt) cc_final: 0.7644 (mtm) REVERT: P 31 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8420 (tptm) outliers start: 19 outliers final: 14 residues processed: 200 average time/residue: 0.5882 time to fit residues: 123.8729 Evaluate side-chains 213 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 85 GLN K 93 GLN K 108 ASN ** M 31 HIS ** 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 = 0.3911 r_free = 0.3911 target = 0.128233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102496 restraints weight = 15718.300| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.52 r_work: 0.3381 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9282 Z= 0.171 Angle : 0.693 11.756 13477 Z= 0.400 Chirality : 0.047 0.218 1536 Planarity : 0.006 0.069 944 Dihedral : 30.993 165.057 2968 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.12 % Allowed : 29.06 % Favored : 66.82 % 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: 2.52 (0.37), residues: 512 helix: 2.39 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.64 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 35 TYR 0.037 0.002 TYR P 88 PHE 0.013 0.001 PHE K 78 HIS 0.004 0.000 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.17 ( 9282) covalent geometry : angle 0.69326 / 0.40 (13477) hydrogen bonds : bond 0.05470 / 6.06 ( 561) hydrogen bonds : angle 2.84028 / 3.91 ( 1382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: K 131 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8384 (mtt-85) REVERT: M 61 GLU cc_start: 0.8047 (mp0) cc_final: 0.7780 (mp0) REVERT: M 64 GLU cc_start: 0.8111 (tp30) cc_final: 0.7574 (tp30) REVERT: M 68 ASN cc_start: 0.8416 (m-40) cc_final: 0.7396 (m-40) REVERT: N 39 TYR cc_start: 0.8518 (t80) cc_final: 0.8314 (t80) REVERT: N 64 ASN cc_start: 0.8827 (m-40) cc_final: 0.8577 (m-40) REVERT: N 73 GLU cc_start: 0.8484 (tp30) cc_final: 0.8220 (tp30) REVERT: O 97 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8076 (mm-30) REVERT: P 31 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8421 (tptm) outliers start: 18 outliers final: 12 residues processed: 201 average time/residue: 0.4949 time to fit residues: 104.9340 Evaluate side-chains 215 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 88 TYR Chi-restraints excluded: chain P residue 90 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 85 GLN K 108 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.128087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102237 restraints weight = 15785.489| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.52 r_work: 0.3378 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9282 Z= 0.179 Angle : 0.691 8.376 13477 Z= 0.397 Chirality : 0.046 0.218 1536 Planarity : 0.006 0.062 944 Dihedral : 30.976 165.888 2968 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.43 % Allowed : 30.43 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.37), residues: 512 helix: 2.42 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.60 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 35 TYR 0.040 0.002 TYR P 88 PHE 0.013 0.001 PHE K 78 HIS 0.001 0.000 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.18 ( 9282) covalent geometry : angle 0.69051 / 0.40 (13477) hydrogen bonds : bond 0.05456 / 6.02 ( 561) hydrogen bonds : angle 2.83005 / 3.90 ( 1382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.196 Fit side-chains REVERT: K 125 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: K 131 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8423 (mtt-85) REVERT: M 61 GLU cc_start: 0.8025 (mp0) cc_final: 0.7769 (mp0) REVERT: M 64 GLU cc_start: 0.8085 (tp30) cc_final: 0.7595 (tp30) REVERT: M 68 ASN cc_start: 0.8401 (m-40) cc_final: 0.7430 (m-40) REVERT: N 64 ASN cc_start: 0.8842 (m-40) cc_final: 0.8594 (m-40) REVERT: N 73 GLU cc_start: 0.8494 (tp30) cc_final: 0.8282 (tp30) REVERT: O 97 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8123 (mm-30) REVERT: P 31 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8432 (tptm) REVERT: P 84 MET cc_start: 0.8125 (tpt) cc_final: 0.7068 (tmt) outliers start: 15 outliers final: 10 residues processed: 203 average time/residue: 0.5092 time to fit residues: 109.0211 Evaluate side-chains 215 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 85 GLN K 108 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN O 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.128210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102584 restraints weight = 15804.813| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.56 r_work: 0.3373 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9282 Z= 0.195 Angle : 0.723 12.242 13477 Z= 0.409 Chirality : 0.047 0.220 1536 Planarity : 0.006 0.068 944 Dihedral : 30.971 165.487 2968 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.97 % Allowed : 31.58 % Favored : 65.45 % 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: 2.49 (0.37), residues: 512 helix: 2.41 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.70 (0.48), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 20 TYR 0.043 0.002 TYR P 88 PHE 0.011 0.001 PHE K 78 HIS 0.002 0.000 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.20 ( 9282) covalent geometry : angle 0.72325 / 0.41 (13477) hydrogen bonds : bond 0.05588 / 6.13 ( 561) hydrogen bonds : angle 2.89656 / 4.08 ( 1382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.218 Fit side-chains REVERT: K 125 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: K 131 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (mtt-85) REVERT: L 45 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.7900 (mtp-110) REVERT: M 61 GLU cc_start: 0.8070 (mp0) cc_final: 0.7803 (mp0) REVERT: M 64 GLU cc_start: 0.8126 (tp30) cc_final: 0.7599 (tp30) REVERT: M 68 ASN cc_start: 0.8410 (m-40) cc_final: 0.7444 (m-40) REVERT: N 64 ASN cc_start: 0.8848 (m-40) cc_final: 0.8591 (m-40) REVERT: N 73 GLU cc_start: 0.8529 (tp30) cc_final: 0.8326 (tp30) REVERT: N 96 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: O 97 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8158 (mm-30) REVERT: P 31 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8516 (tptm) REVERT: P 88 TYR cc_start: 0.8336 (m-10) cc_final: 0.8107 (m-10) outliers start: 13 outliers final: 10 residues processed: 205 average time/residue: 0.5183 time to fit residues: 111.9906 Evaluate side-chains 216 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 30.0000 chunk 33 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 85 GLN K 108 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN O 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.126982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100674 restraints weight = 15760.482| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.52 r_work: 0.3352 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9282 Z= 0.215 Angle : 0.723 9.521 13477 Z= 0.412 Chirality : 0.048 0.221 1536 Planarity : 0.006 0.067 944 Dihedral : 30.975 164.247 2968 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.20 % Allowed : 31.12 % Favored : 65.68 % 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: 2.38 (0.37), residues: 512 helix: 2.37 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 20 TYR 0.042 0.002 TYR P 88 PHE 0.014 0.001 PHE K 78 HIS 0.002 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.21 ( 9282) covalent geometry : angle 0.72283 / 0.41 (13477) hydrogen bonds : bond 0.05851 / 6.41 ( 561) hydrogen bonds : angle 2.94072 / 4.11 ( 1382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.78 seconds wall clock time: 60 minutes 1.11 seconds (3601.11 seconds total)